Program : MOLEMAN
Version : 961218
Author : Gerard J. Kleywegt, Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 590,
SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : manipulation and analysis of PDB files
Package : X-UTIL
Reference(s) for this program:
* 1 * G.J. Kleywegt (1992-1999). Uppsala University, Uppsala, Sweden. Unpublished program.
* 2 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
921022 - ability to produce plot files of temperature factors or
occupancies, averaged over the side-chain atoms (will
give 0.0 for glycyl residues)
921022 - you may now specify a zone of residues with the WRIT
option (useful when breaking up your file in pieces for
X-PLOR: set the protein X-PLOR id, write protein residues,
set the water X-PLOR id, write the waters, etc.)
921022 - definition on main-chain atoms changed; these now include:
N, CA, C, O, OT1 and OT2 (for compatibility with X-PLOR)
930118 - new option: apply_random_rotation
930202 - finally removed the well-known but little-understood bug
which causes MOLEMAN to sometimes write incomplete
PDB files; reason: output file is not closed until next
file is opened and therefore the output buffer isn't flushed
properly; remedy: close file after WRITe_pdb_file ...
930205 - X-PLOR doesn't like SCALE, CRYST and ORIGX cards, so there
is a new question for WRITe_pdb: write non-ATOM/non-REMARK
cards or not ? Reply Y for CCP4, N for X-PLOR
930206 - new option: suggest_ot2; using standard geometry, the program
can suggest coordinates for OT1 and OT2 oxygens which are
needed by X-PLOR (you have to edit them in yourself !)
- new option: list_residue; prints all atoms which have the
residue number (!) that you type
930211 - new option GEOMetry_list; reorganised list of options;
new manual; VERSION 3.0
930212 - added GEOM options 4 and 5
930214 - ask for chain id in WRITE_PDB; new options SEQUence_list,
EXPOrt_bad_file, SAME_export, IMPOrt_bad_file
930222 - options ROTAte_molecule and TRANslate_molecule
930305 - options RAMAchandran and BALAsubramanian
930415 - MERLOT rotation angles in ROTAte; proper handling of CRYST,
and SCALE cards; new option CRYS to set the cell
930519 - inserted error trap for reading ATOM cards
930616 - new option B_Q_statistics
930618 - new options FRAC and CART to move between fractional
and cartesian coordinates; VERSION 4.0
930623 - new option PLAN checks peptide planarity; also recognises
"Bioym hydrogens" (1H, 2H and 3H)
930805 - inclusion of hydrogen atoms made optional for B_Q_STAT;
new option ALWYn_format_read
930823 - removed minor bug in PLOT (time stamp went to fort.14
instead of the per_residue plot file)
930930 - new PIR_sequence_file option
931006 - recognise HETATM cards; recognise the following (store
as REMARK cards): REMARK HEADER COMPND SOURCE REVDAT
SEQRES HELIX SHEET MASTER FORMUL; make output of
REMARK etc cards optional; new option REMA to list
all current REMARK etc cards; VERSION 4.6
931109 - option to analyse disulfide geometry added to GEOM
940214 - 4.7.0 - cleaned up for manual
940307 - 4.7.1 - new option XID_to_chain will "translate" X-PLOR
labels to chain ids
940316 - 4.7.2 - new option O2XHydrogens to fix X-PLOR hydrogen
names for Asn and Arg after mutilation by O
940323 - 4.8 - new option AUTO_chain_segid to generate
different chain and X-PLOR segids for separate
stretches of residues
940415 - 4.9 - improved O2D plot files
940803 - 5.0 - WRITe option allows you to create poly-Gly or
poly-Ser as well; WRITe option allows you to strip X-PLOR
OT1/2 oxygens (replace by one " O " for the benefit of O);
the following options now operate on a zone of residues:
TEMP, LIMI, XPLO, OCCU and CHAI
940812 - 5.0.1 - GEOM now asks you if you want to see the complete
distance matrix and/or the list of bonded distances
940814 - 5.0.2 - debugged WRITe option poly-Serine (didn't handle
Ser, Thr and Cys properly)
940815 - 5.0.3 - changed WRITing of X-PLOR OT1/OT2 (now either keep
them, or replace them by O/OTX)
940816 - 5.1 - new options ORIGin_move and MIRRor_zone
940817 - 5.1.1 - new option INVErt_zone; extended B_Q_statistics
to have separate entry for a ligand or substrate
940829 - 5.1.2 - added option to WATEr_sort to retain residue IDs etc.
940906 - 5.2.0 - new command BONDed_Bs to calculate RMSD and corr.
coeff. of the temperature factors of bonded atoms
941219 - 5.3.0 - new command NONBonded_Bs to calculate RMSD and
corr. coeff. of the Bs of non-bonded atoms
941223 - 5.4 - new FLAG command
941230 - 5.5 - new CA_Ramachandran_plot command
950101 - 5.5.1 - changed AUTO to generate no more than 26 chains (A-Z)
950102 - 5.6 - new CHI_list command
950124 - 5.7 - new DISUlfide_ODL_file command
950201 - 5.7.1 - changed AUTO command such that all subsequent waters
get the same chain/X-PLOR ID (this allows for gaps
in the water residue numbering)
950207 - 5.8 - new GLYco_site command to list potential
N-glycosylation sites (Asn-X-Ser/Thr)
950215 - 5.8.1 - removed bug from NONB option for all atoms
950223 - 5.8.2 - new SMOOth_Bs command
950227 - 5.8.3 - omit Asn-PRO-Ser/Thr as potential N-glycosylation
sites in GLYCo
950311 - 5.9 - new FIT_water_macro command
950330 - 5.9.1 - minor bug fix (write OXT instead of OTX)
950331 - 5.9.2 - new option FROM_chain_to_XID to translate chain labels
into X-PLOR segment IDs
950412 - 5.9.3 - implement per-residue RMS (B or Q) in PLOT option
950413 - 5.9.4 - COUNt_elements option to count chemical elements;
TALLy_residues option to count residue types
950417 - 5.9.5 - new options to makeusing O easier: RSFIt_datablock,
RSR_datablock, CONNect_file, and TORSion_datablock
950421 - 5.9.6 - new option BURIed_charges to assess how well charges
are balanced in the proteins
950505 - 5.9.7 - new option DISTance_distribution to help decide on
suitable Patterson integration limits for rotation
function calculations
950506 - 6.0 - new options CHECk_nomenclature and CORRect_nomenclature
to see if side-chain atoms have been numbered 1/2
correctly
950530 - 6.0.1 - added option to produce polar Ramachandran plots to
the RAMA command
950609 - 6.0.2 - TALLy now also prints % of each residue type; put some
parts of the main program into subroutines so that the
ESV version will compile again ;-)
950614 - 6.0.3 - option SHORt to print short distances
950621 - 6.0.4 - removed bug from RAMA and BALA commands which
calculated "phi" and "psi" angles for N and C
terminal residues at chain breaks ;-) (Look on
it from the bright side: your Ramachandran plot
can only get better !)
950630 - 6.1 - option EXTI to estimate the extinction coefficient
at 280 nm
950705 - 6.2 - new option NO_H_read to strip hydrogen atoms while
reading a PDB file; reorganised list of commands
950715 - 6.3 - new RADIal_B_plot option; print elapsed CPU time if
this exceeds one second; new options HELIx_generate
and STRAnd_generate to generate ideal helices or
strands given two end points
950723 - 6.3.1 - minor bug fix (writing out a single chain didn't work)
950829 - 6.3.2 - print radius of gyration, sum of masses and centre
of mass in STAT command;
edit spacegroup name and value of Z in CRYS command;
new SSBO(nd) command to add SSBOND PDB records
950922 - 6.3.3 - removed bug from O dictionary generation options which
would cause a core dump for ligands of more than 51 atoms;
PLANar_peptides option now skips non-connected (but
sequential) residues; it also prints a warning when
a peptide is CIS (|omega| < 30), or distorted
(30 < |omega| < 150).
950923 - 6.4 - the CA_Ramachandran plot option now also lists (when you
select a PostScript output file) how many residues are in
core, additional, generous and disallowed regions of this
plot
950928 - 6.5 - added CACA_distance command to list statistics about
CA-CA distances
950929 - 6.5.1 - added statistics to CACA command
951010 - - changed lay-out of manual for easy conversion to HTML
951030 - 7.0 - disulfide links are no longer flagged as "bad" contacts
in SHORt_contacts; REMARK records are added with the
following commands: CACA_distances, CA_Ramachandran,
SHORt_contacts, BONDed_Bs, NONBonded_Bs, B_Q_stats;
the B_Q_stats command can now be run on all chains
or just on one (e.g., if you have a protein-protein
complex this is useful to get separate B-factor
statistics for both proteins); the B_Q_stats command
now also lists the maximum B-factor in each category;
waters are now automatically recognised by B_Q_;
you can enter more than one residue type name for
ligands/substrates in the B_Q_ command
951102 - 7.1 - new ASK_auto_chain_segid command
951110 - 7.1.1 - removed bug from text output file with Phi/Psi values
960208 - 7.1.2 - new DUMP_pdb_file command (same as WRITe but no
questions aked other than the file name; other
settings same as in last WRITe)
960209 - 7.2 - added new favoured regions to Ramachandran plot
(PostScript files only)
960405 - 7.2.1 - fixed some instances where ASCII(0) was written
to output PDB files
960415 - 7.2.2 - minor bug fixes
960712 - 7.2.3 - use two cut-offs for bonded atoms for O dictionary
generation commands
961121 - 7.2.4 - minor bug fix
961218 - 7.2.5 - minor bug fix (Ramachandran crashed sometimes on Alphas)
Now that MOLEMAN2 is available, this program has become largely obsolete. Most of the functionality has been implemented in the new program, except for a few exotic ones. Also, many improvements and bug fixes have been made for MOLEMAN2, but not for this program. Hence, unless you want to use one of the few options not (yet) available in MOLEMAN2, use of this program is discouraged. It will not be developed further in the future, although it will remain available for those few exotic options (or users ;-).
? - list available options
! - comment (used in scripts)
QUIT - stop working with the program
READ_pdb_file - PDB formats: standard, Alwyn, X-PLOR
these are automatically recognized
NO_H_read - read PDB file and strip hydrogens
ALWYn_format_read - read mixed-format PDB file
APPEnd_pdb_file - read another PDB file without removing the
atoms already in memory; this is handy when
you want to collect various X-PLOR output PDB
files (protein, ligand, waters) into one model
PDB file for use with "O"
WRITe_pdb_file - almost in standard PDB format; lots of options;
check the example below
DUMP_pdb_file - same as WRITe, but no questions asked
SPLIt_pdb_file - write separate chains to separate files; NONE
of the options of the WRITE option are supported here
COUNt_elements - count how many carbons etc are in the molecule
TALLy_residues - count residue types
RENUmber_atoms - renumber ALL atoms; you must provide the
number of the first atom in the NEW order
(usually, but not always, 1)
RESIdu_renumber - renumber ALL residues; you must provide the
number of the first residue in the NEW order
(usually, but not always, 1)
ZONE_renumber - renumber a range of residues
TEMP_factors_set - alter them using: TFnew = A * TFold + B
AVERage_temp_factors - over (1) all atoms, (2) per residue/all atoms,
(3) per residue/main and side chain separately,
(4) over different chains
OCCUpancies - alter them using: OFnew = A * OFold + B
CHAIn_type - set the chain id for all atoms (NOTE: a chain
id consists of 2 characters, e.g., ' A')
TRANslate_molecule - apply an arbitrary translation to
all your coordinates (NOTE: this irreversibly
alters the coordinates; to retrieve the old
ones, read the input PDB file again !); may be
in Cartesian or Fractional coordinates
ROTAte_molecule - rotate your coordinates; you may enter a rotation
matrix or CCP4 Euler angles or CCP4 polar angles
or MERLOT Euler or MERLOT polar angles
APPLy_random_rotation - apply a random rotation to all your coordinates
a random rotation matrix with entries between
-1 and =1 is generated; this matrix is scaled
until its determinant equals 1.0000 (NOTE: this
alters the coordinates; to retrieve the old
ones, read the input PDB file again !)
STATistics - print average, standard deviation, minimum
and maximum of the X-, Y- and Z-coordinates,
the temperature factors and the occupancies
DISTance_distribution - generate distribution of inter-atomic distances
RANDom_shifts - impose random shifts on the X-, Y- and Z-coordinates,
the temperature factors and the occupancies;
if you want an RMS positional shift of 0.5 A,
then use 0.5, 0.5, 0.5 for the maximum X-, Y- and Z-
shifts (NOTE: this irreversibly alters the
coordinates; to retrieve the old ones, read the input
PDB file again !)
PLOT_Bs_or_Qs - create two plot files of the temperature factors OR
the occupancies of all your atoms and averaged over
each residue (either over all or main-chain only atoms);
these files can be plotted and converted into
PostScript format by O2D
RADIal_B_plot - make a plot of the radial distribution of Bs
XPLOr_ids - set 4-character X-PLOR segment id's
XID_to_chain - "translate" a 4-character X-PLOR segment ID into a
2-character chain label
FROM_chain_to_XID - "translate" chain label to X-PLOR segment ID
AUTO_chain_segid - auto-generate chain and X-PLOR segids
ASK_auto_chain_segid - same as AUTO, but ask for ID names
O2XHydrogens - fix X-PLOR hydrogen names for Asn and Arg
ALTEr_residue_name - change, e.g., all 'SOL' to 'HOH' or 'WAT'
CA_Distance_plot - create a plot file (which can be contoured and
converted into PostScript format by O2D) of the
Ca-Ca distances in your molecule(s)
LIMIt_B_and_Q - reset any unrealistic values that may have crept
in; you supply the minimum and maximum allowed
values for the temperature factors and occupancies
and the program resets any values which exceed
these limits
WATEr_sort - collect all waters (hydrogens are assumed to be
ABSENT !!!); make the one with the set of lowest
X, Y and Z coordinates water nr 1, then its
nearest neighbour water nr 2, etc. This should
help (a) to minimise the number of map_draw
operations in "O" and (b) to detect any duplicate
waters (i.e., they're close together or coincide)
NOTE: the X, Y, Z, B and Q are SWAPPED; the
residue names, numbers, etc are not altered,
unless tou specifically request this
FIT_water_macro - generate O macro to do RSR_rigid and RS_fit on all waters
SUGGest_OT2 - suggest coordinates for OT1 and OT2 using the
coordinates of N, CA, C and O, using standard
geometry (bonds, angles, flat carboxylate)
LIST_residue - list all atoms with a given residue number
GEOMetry_list - list geometry of a residue, the N-CA-C backbone,
the CA backbone, two residues (e.g., two neighbours
or two Cysteines in a disulfide bridge) or a zone
of residues
DISUlfide_ODL_file - create an ODL file to draw disulfide bridges in O
SSBOnd - add PDB SSBOND records automatically
GLYCo_site - list potential N-glycosylation sites
RSFIt_datablock - generate O RS-fit datablock for a residue type
RSR_datablock - generate O RSR datablock for a residue type
CONNect_file - generate O connectivity file for a residue type
TORSion_datablock - generate torsion datablock for a residue type
SEQUence_list - list the first atom of every residue (helps
if you forgot the residue numbers of your
waters, etc. etc.)
EXPOrt_bad_file - write a file with INTERNAL (as opposed to Cartesian)
coordinates
SAME_export - ditto, with a previously generated sort order and
connectivity table
IMPOrt_bad_file - read an internal coordinate file
RAMAchandran_plot - guess what
BALAsubramanian_plot - ditto
CHI_list - list CHI1-4 values (where defined)
BURIed_charges - assess charged protein residues
CA_Ramachandran_plot - make a pseudo-Ramachandran plot with CA angles
and dihedrals & list statistics
CACA_distances - print statistics about CA-CA distances
CRYStal_PDB_card - define unit-cell constants
B_Q_statistics - print average B and Q for protein, main-chain, side-chain,
water, other atoms and overall
BONDed_Bs - print RMSD and corr. coeff. of the temperature factors of
bonded atoms
NONBonded_Bs - print RMSD and corr. coeff. of the temperature factors of
non-bonded atoms
SHORt_contacts - print short distances
SMOOth_Bs - smooth B factors for neighbouring atoms
CHECk_nomenclature - check if side-chain 1/2 atoms are named correctly
CORRect_nomenclature - correct any errors in side-chain 1/2 atom names
FRACtional_to_cartesian - guess what
CARTesian_to_fractional - guess again
PLANar_peptides - lists peptide impropers
PIR_sequence_file - make a PIR sequence file using the
residues in your current protein
REMArk_etc_cards - list all REMARK, HEADER etc. cards that
are currently in memory
ORIGin_move - move the centre-of-gravity of a zone of residues
to (0,0,0)
MIRRor_zone - mirror one or more residues in the YZ, XZ or XY
plane to get different chiral enantiomers
INVErt_zone - invert the coordinates of one or more residues
and move the centre-of-gravity back to where
it was
FLAG_colours - generate O datablock for colouring your molecule
according to the colours of a flag
EXTInction_280 - estimate extinction at 280 nm
The program handles canonical PDB files as well as the files that are produced or needed by O, CCP4, X-PLOR and BIOSYM programs. However, only ATOM, HETATM and CRYST1 cards are actually parsed. Some other cards are stored (REMARK etc.), others are ignored.
There is one conflict with PDB conventions and that is that the chain ID may consist of *TWO* characters in MOLEMAN. This can be circumvented by always using a "space" (blank) as the first character of any chain ID you type.
Older versions of O produced "Alwynian PDB files" which had the residue name appended to the chain identifier. The READ and APPEnd options will check the VERY FIRST ATOM in your file to see if it is in "Alwyn's format". If you have MIXED FORMATS (e.g., the protein in standard format and the solvent in Alwyn's format), use the option ALWY to read your PDB file.
The following residue types are recognised as being water molecules by most commands: WAT, HOH, SOL, OHH, HHO, H2O, OH2, H3O, OH3, EAU.
Hydrogen atoms are recognised as such if their atom names start with ' H' (standard PDB convention), 'HH', 'HD', 'HE' (X-PLOR), '1H', '2H', '3H', ' 1H', ' 2H', ' 3H' (BIOSYM and others), or ' Q' (NMR pseudo-atoms).
The first FOUR characters of each command are unique and are the only ones that need to be typed. The program will prompt for any additional input if required, using sensible defaults in most cases.
To run the program in batch mode (gives carriage returns after input prompts and will crash if a file can't be opened), use the "-b" flag as a command-line argument.
Some options produce O2D plot files. These need to be converted into PostScript or CricketGraph format with the program O2D, also part of the X-UTIL suite of programs.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- *** MOLEMAN *** MOLEMAN *** MOLEMAN *** MOLEMAN *** MOLEMAN *** MOLEMAN ***Version - 950929/6.5.1 (C) 1993-5 Gerard J. Kleywegt, Dept. Mol. Biology, BMC, Uppsala (S) User I/O - routines courtesy of Rolf Boelens, Univ. of Utrecht (NL) Others - T.A. Jones, G. Bricogne, Rams, W.A. Hendrickson Others - W. Kabsch, CCP4, PROTEIN, E. Dodson, etc. etc.
Started - Wed Oct 11 01:16:35 1995 User - gerard Mode - interactive Host - onyx ProcID - 19394 Tty - /dev/ttyq17
*** MOLEMAN *** MOLEMAN *** MOLEMAN *** MOLEMAN *** MOLEMAN *** MOLEMAN ***
Reference(s) for this program:
* 1 * [O/X-PLOR DICTIONARIES] G.J. Kleywegt Dictionaries for Heteros ESF/CCP4 Newsletter 31 (32?), June 1995, pp. 45-50
*** MOLEMAN *** MOLEMAN *** MOLEMAN *** MOLEMAN *** MOLEMAN *** MOLEMAN ***
Maximum number of atoms : ( 100000) Maximum number of residues : ( 10000) Max nr of atoms per residue : ( 100) Maximum buffer (words) : ( 524288) Max nr of non-ATOM records : ( 1000)
=> Random number generator initialised with seed : 1
===> INPUT/OUTPUT/CONTROL: ? ! READ_pdb_file NO_H_read ALWYn_format_read APPEnd_pdb_file WRITe_pdb_file SPLIt_pdb_file EXPOrt_bad_file IMPOrt_bad_file SAME_export QUIT HELIx_generate STRAnd_generate
===> MISCELLANEOUS: REMArk_etc_cards CRYStal_PDB_card TALLy_residues COUNt_elements GLYCo_sites EXTInction_280 WATEr_sort PIR_sequence_file SSBOnd_records
===> O FILES: RSR_datablock CONNect_file TORSion_datablock RSFIt_datablock DISUlfide_ODL_file FIT_water_macro FLAG_colours
===> ANALYSIS: STATistics CA_Distance_plot PLOT_Bs_or_Qs LIST_residue GEOMetry_list SEQUence_list RAMAchandran_plot BALAsubramanian_plot CA_Ramachandran_plot CACA_distances PLANar_peptides BURIed_charges DISTance_distribution SHORt_contacts RADIal_B_plot CHI_list
===> TEMPERATURE FACTORS & OCCUPANCIES: LIMIt_B_and_Q AVERage_temp_factors TEMP_factors_set OCCUpancies_set SMOOth_Bs B_Q_statistics BONDed_Bs NONBonded_Bs
===> ATOMS, RESIDUES, CHAINS & SEGMENTS: O2XHydrogens SUGGest_OT2 RENUmber_atoms ALTEr_residue_name RESIdu_renumber ZONE_renumber CHECk_nomenclature CORRect_nomenclature CHAIn_name XPLOr_ids FROM_chain_to_XID XID_to_chain AUTO_chain_segid ASK_auto_chain_segid
===> MANIPULATION OPTIONS: FRACtional_to_cartesian CARTesian_to_fractional ROTAte_molecule TRANslate_molecule APPLy_random_rotation RANDom_shifts ORIGin_move MIRRor_zone INVErt_zone
Option ? (READ_pdb_file) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (?) readInput PDB file ? (in.pdb) 1cel.pdb Number of lines read : ( 7524) Number of atoms now : ( 7038) CPU total/user/sys : 5.0 4.9 0.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ) no_hInput PDB file ? (1cel.pdb) m1_mb.pdb Number of lines read : ( 5864) Hydrogens skipped : ( 1118) Number of atoms now : ( 4742) CPU total/user/sys : 4.2 4.1 0.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (NO_H) appeInput PDB file ? (m1_mb.pdb) 1cel.pdb Number of lines read : ( 7524) Number of atoms now : ( 11780) CPU total/user/sys : 5.0 5.0 0.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Write the current molecule(s) to a PDB file. If the file exists,
an error message is printed and (in interactive mode) you are
asked if you want to overwrite the file, or provide a different
name for it.
One new REMARK card can be added, and all previous REMARK etc. cards
may either be written or ignored.
You may select which chain and/or zone of residues to write out.
To generate molecular replacement models, you can write out all atoms,
main-chain only, poly-Gly, poly-Ala or poly-Ser.
You may either write or skip hydrogen atoms.
The carboxy-terminal oxygens (if they have X-PLOR names) can be written
with different names.
You may include CRYST1 etc. cards (e.g., for CCP4), or omit them (e.g.,
for X-PLOR).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (APPE) writeOutput PDB file ? (out.pdb) m1_mb.pdb ERROR --- XOPXNA - error # 126 while opening NEW file : m1_mb.pdb OPEN : (UNIT= 12 STATUS=NEW CAR_CONTROL=LIST FORM=FORMATTED ACCESS=SEQUENTIAL) Error : (Connection timed out) Open file as OLD (Y/N) ? (N) yes REMARK at start of file ? (MoleMan PDB file) Copy all REMARK, HEADER etc. cards from input ? (Y) Which chain to write (** = any and all) ? (**) Residue range to write (0 0 = all molecule) ? ( 0 0) You may output All atoms, only Main-chain atoms, a Poly-alanine (Gly intact), a poly-Serine, (Gly and Ala intact) or a poly-Glycine Write option do you want (All/M/P/S/G) ? (A) Write HYDROGEN atoms (Y/N) ? (N) Force consecutive atom numbering (Y/N) ? (Y) XPLOR needs OT1 and OT2, but O hates them If your file contains OT1/2 you may either keep them, or replace them by O/OXT Write XPLOR OT1/2 ? (Y/N) ? (N) Cell : ( 84.000 86.200 111.800 90.000 90.000 90.000) CCP4 requires CRYST, SCALE and ORIGX cards XPLOR does not like them at all Therefore: reply Y for CCP4 and N for XPLOR : Write CRYST, SCALE, ORIGX cards (Y/N) ? (Y) Nr of atoms written : ( 11780) CPU total/user/sys : 9.0 8.9 0.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Same as WRITe, but no questions are asked, other than the output file name. All other parameters will have the same values as the last time you used the WRITe command (or the defaults, if you hadn't used WRITe yet).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (DIST) dumpOutput PDB file ? (out.pdb) q.pdb Nr of atoms written : ( 3646) CPU total/user/sys : 2.1 2.1 0.0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Nr of segments found : ( 10) Option ? (AUTO) splitBasename of PDB files ? (out) qqq New chain id : ( A) New pdb file : (qqqa.pdb) Nr of atoms written to it : ( 4226) New chain id : ( B) New pdb file : (qqqb.pdb) Nr of atoms written to it : ( 464) New chain id : ( C) New pdb file : (qqqc.pdb) Nr of atoms written to it : ( 36) ... New chain id : ( J) New pdb file : (qqqj.pdb) Nr of atoms written to it : ( 2) Nr of atoms written in core : ( 11780) CPU total/user/sys : 8.9 8.8 0.2 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (SPLIt) alwyInput PDB file ? (1cel.pdb) OnO !!! It is an "Alwyn-Jones-PDB-file" ... Number of lines read : ( 7524) Number of atoms now : ( 7038) CPU total/user/sys : 5.1 5.1 0.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Use these commands to generate bits of ideal helix/strand. For instance,
if you see a helix in your map, click on two bones atoms at the termini,
feed them into MOLEMAN, and include the helix into your model with O.
The number of residues is figured out by dividing the distance between
the end-points by 1.46 A/residue (helix) or 3.32 A/residue (strand).
If you want to model without experimental data, just multiply the
number of residues that you want to generate by 1.46 or 3.32 and use
that number as the X-coordinate of the end point, with all other
coordinates equal to zero.
NOTE: both these options will ERASE the current molecule from memory !!!
NOTE: the version of the algorithm implemented in MOLEMAN is inferior to the one available in MOLEMAN2. In particular for short stretches this may yield rubbish in this program, but correct results in MOLEMAN2. You are therefore strongly advised to use MOLEMAN2 instead of this program for the generation of helices and strands ! Use the AUto SPink, BOnes or SSe command in MOLEMAN2 instead.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (ALWY) helix WARNING - This will ERASE your current molecule ! Are you sure ? (N) yes Provide the coordinates of the N- and the C- terminal CA atoms (approximately). If you only want to generate X residues, enter 0,0,0 for the N-terminus and: HELIX : 1.46*X,0,0 for the C-terminus, STRAND: 3.32*X,0,0 for the C-terminus Start coordinates (N-term) ? ( 0.000 0.000 0.000) 49.0 62.6 44.4 End coordinates (C-term) ? ( 10.000 10.000 10.000) 56.8 67.7 46.3 Length (A) : ( 9.511) Nr of residues : ( 7) Distance terminal CAs (A) : ( 9.626) All done ... Use Move_zone and RSR_rigid in O to position the structure element into the density; then use Mutate_* and Lego_side_ch for the correct residue types and rotamers. ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (HELIx) strand WARNING - This will ERASE your current molecule ! Are you sure ? (N) y Provide the coordinates of the N- and the C- terminal CA atoms (approximately). If you only want to generate X residues, enter 0,0,0 for the N-terminus and: HELIX : 1.46*X,0,0 for the C-terminus, STRAND: 3.32*X,0,0 for the C-terminus Start coordinates (N-term) ? ( 49.000 62.600 44.400) 48.5 66.3 19.5 End coordinates (C-term) ? ( 56.800 67.700 46.300) 37.7 69.9 35.9 Length (A) : ( 19.964) Nr of residues : ( 7) Distance terminal CAs (A) : ( 19.829) All done ... Use Move_zone and RSR_rigid in O to position the structure element into the density; then use Mutate_* and Lego_side_ch for the correct residue types and rotamers. ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (STRAnd) quit*** MOLEMAN *** MOLEMAN *** MOLEMAN *** MOLEMAN *** MOLEMAN *** MOLEMAN ***
Version - 950929/6.5.1 Started - Wed Oct 11 01:16:35 1995 Stopped - Wed Oct 11 01:26:15 1995
CPU-time taken : User - 37.0 Sys - 0.6 Total - 37.6
*** MOLEMAN *** MOLEMAN *** MOLEMAN *** MOLEMAN *** MOLEMAN *** MOLEMAN ***
>>> This program (C) 1993-95, GJ Kleywegt & TA Jones <<< E-mail: "gerard@xray.bmc.uu.se" or "alwyn@xray.bmc.uu.se"
*** MOLEMAN *** MOLEMAN *** MOLEMAN *** MOLEMAN *** MOLEMAN *** MOLEMAN ***
STOP ... Toodle pip ... statement executed 36.9u 0.6s 9:40 6% 0+0k 144+239io 65pf+0w ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
These options were implemented for use with a new version of AVEPDB which will average coordinate sets based on the internal coordinates (i.e., in terms of distances, angles and dihedrals) of molecules, rather than on their Cartesian coordinates. The rationale for doing this is that the latter will distort the bond distances and angles if two or more structures are considerably different. For example, if you have two diverged molecules after Simulated Annealing, the bonds and angles will be fairly similar in both, but the (less or non-constrained) dihedrals will differ considerably.
By averaging internal coordinates, you retain reasonably good geometry.
=> EXPO will sort the atoms, create a connectivity table, compute the
internal coordinates and create a file;
=> SAME will use the connectivity generated in a previous EXPO step and
use it to generate an internal coordinates file;
=> IMPO will read an internal coordinates file and convert the coordinates
back to the Cartesian system.
NOTE: using EXPO and IMPO subsequently effectively sorts the atoms in your
file, BUT it also puts the first atom at (0,0,0) !!! I.e., if you don't
want that, use the lsq-options in O to transform the sorted molecule
back to its original position and orientation in space. In addition,
you will loose all non-ATOM records you had before as well as the
information stored beyond the occupancies in the PDB files (such as
atomic numbers and X-PLOR id's)
NOTE: atoms for each residue are sorted as follows: first come N, CA, C, O,
OT1 and OT2 (whichever are present); next the non-hydrogen atoms are
sorted according to the "Greek alphabet" using the third and fourth
characters of the atom names (i.e., " CG " comes BEFORE " CD " !);
finally, the hydrogens are sorted similarly
NOTE: if you want to convert several files for use with the new AVEPDB
version, first of all make sure that all files contain the SAME set
of atoms; then make sure they are in the same order (use EXPO and then
IMPO if the order is different); READ the first molecule, EXPOrt it,
READ the second molecule, use SAME_export etc. Don't use ANY OTHER
options in the mean time, or you might screw up the connectivity
data (they are stored in a volatile buffer array) !!!
NOTE: suggested file extension for internal coordinate files is ".bad",
for Bond, Angles, Dihedrals
An internal coordinate file looks as follows (the first line is not part of the file; it shows what each column contains):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- KEY ATOM-NR TYPE RES NAME DIST ANGLE DIHEDR OCC B-FAC I1 I2 I3 BAD 1 N PRO 2 0.000 0.000 0.000 1.00 20.00 0 0 0 BAD 2 CA PRO 2 1.483 0.000 0.000 1.00 20.00 1 0 0 BAD 3 C PRO 2 1.544 116.750 0.000 1.00 20.00 2 1 0 BAD 4 O PRO 2 1.240 118.965 -58.380 1.00 20.00 3 2 1 ... BAD 1089 N GLU 133 1.342 125.081 144.087 1.00 20.00 1085 1084 1083 BAD 1090 CA GLU 133 1.471 117.547-167.337 1.00 20.00 1089 1085 1084 BAD 1091 C GLU 133 1.496 118.182-149.730 1.00 20.00 1090 1089 1085 BAD 1092 OT1 GLU 133 1.233 117.554 119.898 1.00 20.00 1091 1090 1089 BAD 1093 OT2 GLU 133 1.230 117.243 -62.811 1.00 20.00 1091 1090 1089 BAD 1094 CB GLU 133 1.496 108.563 87.927 1.00 20.00 1090 1089 1085 BAD 1095 CG GLU 133 1.510 123.211-167.204 1.00 20.00 1094 1090 1089 BAD 1096 CD GLU 133 1.522 104.605 174.176 1.00 20.00 1095 1094 1090 BAD 1097 OE1 GLU 133 1.237 118.296 88.019 1.00 20.00 1096 1095 1094 BAD 1098 OE2 GLU 133 1.230 117.804 -89.234 1.00 20.00 1096 1095 1094 BAD 1099 H GLU 133 0.976 122.606 18.116 1.00 0.00 1089 1085 1084 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
I1 = the atom-nr of the atom to which the distance is defined;
I2 = the angle is defined from the current atom via I1 to I2;
I3 = ditto, for the dihedral: current - I1 - I2 - I3
The program is clever enough to use mostly bonded distances, except for the first residue of every separate entity (chain, ligand, waters):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... BAD 1789 CE1 PHE A 221 1.377 120.623 178.691 1.00 60.54 1787 1786 1785 BAD 1790 CE2 PHE A 221 1.379 118.651-178.655 1.00 60.54 1788 1786 1785 BAD 1791 CZ PHE A 221 1.385 121.139 -0.033 1.00 60.54 1790 1788 1786 BAD 1792 N GSB A 300 2.992 122.117 49.893 1.00 21.23 534 532 531 BAD 1793 CA GSB A 300 1.441 93.410 52.446 1.00 21.23 1792 534 532 BAD 1794 C GSB A 300 1.509 109.221 -90.973 1.00 21.23 1793 1792 534 ... BAD 1818 CYY GSB A 300 1.382 121.935 -0.091 1.00 25.29 1817 1816 1813 BAD 1819 O1 HOH A 401 2.596 145.966 164.959 1.00 36.12 1187 1186 1185 BAD 1820 O1 HOH A 402 2.556 108.456 -85.671 1.00 28.22 1233 1232 1229 ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (STATs) readInput PDB file ? (m3b.pdb) m3a.pdb Number of lines read : ( 1104) Number of atoms now : ( 1099) Option ? (READ) expo
Output Bonds/Angles/Dihedrals file ? (m3a.bad) m3a.bad ERROR --- XOPXNA - error # 126 while opening NEW file : m3a.bad Open file as OLD (Y/N) ? (N) y Nr of atoms sorted : ( 1099) ... I am toiling ...
Option ? (EXPO) read
Input PDB file ? (m3a.pdb) m3b.pdb Number of lines read : ( 1104) Number of atoms now : ( 1099) Option ? (READ) same
Output Bonds/Angles/Dihedrals file ? (m3a.bad) m3b.bad ERROR --- XOPXNA - error # 126 while opening NEW file : m3b.bad Open file as OLD (Y/N) ? (N) y
Option ? (SAME) impo
Input Bonds/Angles/Dihedrals file ? (m3b.bad) m3a.bad Nr of lines read : ( 1099) Nr of atoms read : ( 1099) ... Converting to Cartesian coordinates ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ_pdb_file) remark # 1 > HEADER HYDROLASE(O-GLYCOSYL) 17-MAY-94 1CEL 1CEL 2 # 2 > COMPND 1,4-BETA-D-GLUCAN CELLOBIOHYDROLASE I (CELLULASE) 1CEL 3 # 3 > COMPND 2 (E.C.3.2.1.91) 1CEL 4 # 4 > SOURCE FUNGUS (TRICHODERMA REESEI) 1CEL 5 # 5 > AUTHOR C.DIVNE,T.A.JONES 1CEL 6 # 6 > REVDAT 1 01-NOV-94 1CEL 0 1CEL 7 # 7 > JRNL AUTH C.DIVNE,J.STAHLBERG,T.REINIKAINEN,L.RUOHONEN, 1CEL 8 ... #286 > SSBOND 20 CYS B 261 CYS B 331 1CEL 359 #287 > MTRIX1 1 1.000000 0.000000 0.000000 -38.09200 1 1CEL 371 #288 > MTRIX2 1 0.000000 1.000000 0.000000 -43.10800 1 1CEL 372 #289 > MTRIX3 1 0.000000 0.000000 1.000000 -56.39300 1 1CEL 373 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Define the unit cell constants. These may be written as a CRYST1 card in output PDB files; SCALEX cards are derived from the cell constants; ORIGX cards are always set to the identity operator.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (REMArk) cryst Unit-cell constants ? ( 84.000 86.200 111.800 90.000 90.000 90.000) Unit-cell volume (A3) : ( 8.095E+05) Spacegroup ? (P 21 21 2) Value of Z ? ( 8) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (CRYSt) tally Type PCA Number = 2 ( 0.14 %) Type SER Number = 100 ( 7.12 %) Type ALA Number = 54 ( 3.85 %) Type CYS Number = 40 ( 2.85 %) Type THR Number = 92 ( 6.55 %) ... Type PHE Number = 30 ( 2.14 %) Type MET Number = 12 ( 0.85 %) Type NAG Number = 2 ( 0.14 %) Type IBZ Number = 2 ( 0.14 %) Type GLC Number = 2 ( 0.14 %) Type CA Number = 1 ( 0.07 %) Nr of waters found : ( 529) (Using the most usual names for waters) Total nr of residues : ( 1404) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ) tally Nr of " T" residues : ( 5) Nr of " C" residues : ( 5) Nr of " A" residues : ( 5) Nr of " G" residues : ( 5) There are *NO* waters Total nr of residues : ( 20) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (TALLy) count Nr of Carbon atoms : ( 3992) There are *NO* Hydrogen atoms Nr of Nitrogen atoms : ( 1068) Nr of Oxygen atoms : ( 1921) Nr of Sulfur atoms : ( 54) There are *NO* Phosphorous atoms Additional elements: Nr of " I" atoms : ( 2) Nr of "CA" atoms : ( 1) Total nr of atoms : ( 7038) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (COUNt) glyco Nr of residues found : ( 1404) Potential N-glycosylation site # 1 : ASN 45 - (not PRO) - SER 47 Potential N-glycosylation site # 2 : ASN 64 - (not PRO) - THR 66 Potential N-glycosylation site # 3 : ASN 270 - (not PRO) - SER 272 Potential N-glycosylation site # 4 : ASN 384 - (not PRO) - THR 386 *NOT* an N-glycosylation site : ASN 431 - PRO - SER 433 Potential N-glycosylation site # 5 : ASN 45 - (not PRO) - SER 47 Potential N-glycosylation site # 6 : ASN 64 - (not PRO) - THR 66 Potential N-glycosylation site # 7 : ASN 270 - (not PRO) - SER 272 Potential N-glycosylation site # 8 : ASN 384 - (not PRO) - THR 386 *NOT* an N-glycosylation site : ASN 431 - PRO - SER 433 Potential glycosylation sites : ( 8) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ) ssbo Max SS bond length (A) ? ( 2.500) 2.225 SG CYS A 4 36.618 67.989 34.228 1.00 21.90 1CEL 398 148 SG CYS A 19 46.720 75.194 72.769 1.00 16.00 1CEL 521 181 SG CYS A 25 47.360 76.947 73.550 1.00 18.46 1CEL 554 ... 5989 SG CYS B 331 -7.298 9.647 20.243 1.00 10.03 1CEL6363 6482 SG CYS B 397 -25.330 24.877 13.503 1.00 10.62 1CEL6856
Nr of CYS SG atoms found : ( 40)
SSBOND 1 CYS A 4 CYS A 72 S-S = 2.03 A SSBOND 2 CYS A 19 CYS A 25 S-S = 2.02 A ... SSBOND 19 CYS B 238 CYS B 243 S-S = 2.03 A SSBOND 20 CYS B 261 CYS B 331 S-S = 2.03 A
Nr of disulfide bridges : ( 20) Option ? (SSBO) ssbo ERROR --- SSBOND records already present ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (SSBO) exti Reference: Gill & Von Hippel, Anal. Biochem. 182: 319-326 (1989). e280 = (1280*TYR + 5690*TRP + 120*CYS) accuracy roughly 5%; units M-1 cm-1 Nr of residues : ( 868) Nr of TYR : ( 40) Nr of TRP : ( 18) Nr of CYS : ( 40) e280 (M-1 cm-1) ~ ( 1.584E+05) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Sort your waters so that each water gets its nearest
neighbour as its successor in the list of atoms; the
printed distances reveal water molecules which you
have put in more than once (or extremely close to
one another; if a distance is less than 2.5 A, a
warning message is printed).
NOTE: your file should NOT contain any water-hydrogen atoms !!!
Optionally, you may also swap residue IDs etc., but
this will mean that your waters are not sorted by
ID any longer after this operation !!
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ_pdb_file) water What have you called your waters ? (HOH) You may either swap XYZ,B,Q only, OR also swap residue numbers etc.; in the latter case, your waters may *NOT* be sorted by residue ID afterwards !!! Swap residue numbers etc. ? (N) y Nr of water molecules found : ( 100) Water molecule with minimum coordinates : ( 61) ... swap waters 300 and 360 Closest water is : ( 380) Distance (A) : ( 4.237) ... swap waters 301 and 380 Closest water is : ( 331) Distance (A) : ( 4.568) ... swap waters 302 and 331 Closest water is : ( 317) Distance (A) : ( 2.988) ... swap waters 303 and 317 ... ... swap waters 311 and 398 Closest water is : ( 315) Distance (A) : ( 7.679) ... swap waters 311 and 315 Nr of waters sorted : ( 100) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 50 gerard rigel 23:39:23 progs/moleman > grep atom watersorted.pdb ATOM 1 O1 HOH 360 11.358 8.880 19.119 1.00 24.31 8 ATOM 2 O1 HOH 380 11.561 10.834 22.873 1.00 43.23 8 ATOM 3 O1 HOH 331 10.555 13.666 26.313 1.00 32.55 8 ATOM 4 O1 HOH 317 13.212 14.450 25.193 1.00 18.03 8 ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Generate a PIR sequence file from your current molecule. Unrecognised residue types (e.g. solvent, ligand) give rise to a SPACE, but if these residues FOLLOW your protein residues, no harm is done.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (WATEr) pir_ Amino acid residue names ? (ALA ARG ASN ASP CYS GLN GLU GLY HIS ILE LEU LYS MET PHE PRO SER THR TRP TYR VAL CPR ASX GLX UNK) One letter codes ? (A R N D C Q E G H I L K M F P S T W Y V J B Z X) PIR output file name ? (sequence.pir) PIR sequence name ? (SEQUENCE) PIR sequence title ? (Any title) Number of residues encountered : ( 1404) Recognised one-letter codes : ( 866) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 156 gerard rigel 15:46:09 progs/moleman > cat sequence.pir ! Created by MOLEMAN V. 930930/4.5 at Thu Sep 30 16:28:42 1993 for user gerard>P1;SEQUENCE test pir FPTIPLSRLF DNAMLRAHRL HQLAFDTYQE FEEAYIPKEQ KYSFLQNPQT SLCFSESIPT PSNREETQQK SNLELLRISL LLIQSWLEPV QFLRSVFANS LVYGASDSNV YDLLKDLEEG IQTLMGRLED GSPRTGQIFK QTYSKFDTNS HNDDALLKNY GLLYCFRKDM DKVETFLRIV QCRSVEGSCG * ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (RSFIt) rsr_ Which residue number ? ( 200)1092 C1 RTA 200 21.972 29.831 16.739 1.00 15.25 6 1093 C2 RTA 200 20.921 30.524 15.841 1.00 15.61 6 ... 1113 O22 RTA 200 21.840 21.712 27.037 1.00 10.99 8
Nr of atoms found : ( 22) Residue type : (RTA) Atom types : ( C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 C20 O21 O22) Datablock file ? (rsr_dict_rta.odb) Datablock name : (RSR_dict_RTA) Datablock written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Created by MOLEMAN V. 950417/5.9.5 at Mon Apr 17 23:03:29 1995 for user gerard ! ! RSR datablock for RTA ! RSR_dict_RTA T 2 70 C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 C20 O21 O22 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Generate an O connectivity file for a residue type (append to your standard connectivity file, or read directly into O with the Conn_file command). Hydrogen-hydrogen "bonds" are automatically removed.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (CONN) Which residue number ? ( 223) Cut-off distance for bonded atoms ? ( 1.000) 1.91797 N1 GSB A 223 77.464 26.288 13.425 1.00 21.20 1GUH1918 1798 CA1 GSB A 223 78.377 27.299 12.928 1.00 21.20 1GUH1919 ... 1822 O31 GSB A 223 81.410 34.774 18.220 1.00 21.20 1GUH1943 1823 O32 GSB A 223 81.064 32.646 18.148 1.00 21.20 1GUH1944
Nr of atoms found : ( 27) Residue type : (GSB) Atom types : ( N1 CA1 C1 O11 O12 CB1 CG1 CD1 OE1 N2 CA2 C2 O2 CB2 SG2 CD2 CE2 CF1 CF2 CZ1 CZ2 CYY N3 CA3 C3 O31 O32) Connect file ? (connect_gsb.dat) Nr of bonds : ( 27) Nr of ATOM records : ( 3) Nr of CONNECT ,, : ( 7) Connect file written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- GSB ATOM N1 CA1 C1 O11 O12 CB1 CG1 CD1 OE1 N2 ATOM CA2 C2 O2 CB2 SG2 CD2 CE2 CF1 CF2 CZ1 ATOM CZ2 CYY N3 CA3 C3 O31 O32 CONNECT - N1 CA1 C1 O11 + CONNECT CA1 CB1 CG1 CD1 OE1 CONNECT C1 O12 CONNECT CD1 N2 CA2 C2 O2 CONNECT CA2 CB2 SG2 CD2 CE2 CF1 CZ1 CYY CZ2 CF2 CE2 CONNECT C2 N3 CA3 C3 O31 CONNECT C3 O32 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Generate a torsion datablock (for use with the Tor_residue command in O).
This appears to be a simple exercise, but it is not. Consider all-
trans-retinoic acid with 22 atoms and 22 bonds. This yields more than
40 dihedral angles, but only 3 torsion entries ... The trick is to
throw away every dihedral which appears to be strongly restrained,
dihedrals inside rings, etc. MOLEMAN uses the following criteria
to reduce the number of torsions:
- any dihedral which is equal to -180, 0 or +180 degrees (with a
tolerance of 5 degrees) is rejected as (probably) being strongly
restrained to its current value (e.g., in conjugated systems)
- any dihedral K->I->J->L whose rotation affects atom "K" or
"I" is rejected as (probably) being part of a ring system
- if the number of atoms affected by the torsion is >= the total
nr of atoms minus 4, the torsion is rejected. In this case,
(for example, a torsion involving a carboxylate) it makes more
sense to use the torsion defined the other way around (i.e.,
use torsion L-J-I-K which affects only 1 or 2 atoms, instead of
K-I-J-L)
- if a torsion is around the same bond as a previous torsion, and
it affects the same atoms as that previous torsion, it is rejected
as being a simple permutation. This happens, for instance, for
carboxylates and for aliphatic tails sprouting from a ring, in
which case there are two equivalent ways to define the torsion
of the tail relative to the ring)
The "surviving", freely rotatable torsion angles are written to a file. This file must be *appended* to your standard torsion file (ODAT/torsion.o, for instance), and the number of lines in the datablock must be updated accordingly.
Note that this option doesn't know anything about linkages to other residues (and therefore is less suited for use with oligomeric compounds). For instance, if you run it on a TRP residue, you'll get several unwanted torsions:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- RESIDUE TRP TORSION TOR1 -58. N CA CB CG CG CD2 CE2 CE3 CD1 NE1 CZ2 CZ3 CH2 TORSION TOR2 -40. N CA C O O TORSION TOR3 -58. CG CB CA N N C O TORSION TOR4 -99. CA CB CG CD2 CD2 CE2 CE3 CD1 NE1 CZ2 CZ3 CH2 TORSION TOR5 -99. CD2 CG CB CA N CA C O ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
TOR1 is simply CHI1; TOR2 would be deleted; TOR3 is CHI1 in reverse; TOR4 is CHI2 and TOR5 is CHI2 in reverse. Hence, for oligomeric compounds (with distinct residues, that is; it will work fine for glutathione if this is treated as a single residue; check for example residue 223 in PDB entry 1GUH) one would have to add torsions involving neighbouring residues, and probably delete some non-standard torsions.
Note: at present, O can only handle a maximum of 12 torsion angles. This means you may have to remove some of them (but remember that many of them will be defined in two ways, so you can keep the one you find most useful of each such pair).
The following example shows how this works for retinoic acid (residue 200 in PDB entry 1CBS if you want to try it at home). Note that indeed only the three intuitively reasonable torsions are generated: the tail relative to the ring, the ring relative to the tail, and the carboxylate relative to the tail !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- All-trans-retinoic is (incorrectly ;-) numbered as follows:C16 C19 C20 O21 | | | / C5 C7 C9 C11 C13 C15 /\\ / \\ / \\ / \\ / \\ / \ C4 C6 C8 C10 C12 C14 O22 | | C3 C1--C17 \ /\ C2 C18
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (TORS) Which residue number ? ( 7) 200 Cut-off distance for bonded atoms ? ( 2.000)1092 C1 RTA 200 21.972 29.831 16.739 1.00 15.25 6 1093 C2 RTA 200 20.921 30.524 15.841 1.00 15.61 6 ... 1112 O21 RTA 200 23.640 21.075 25.978 1.00 13.29 8 1113 O22 RTA 200 21.840 21.712 27.037 1.00 10.99 8
Nr of atoms found : ( 22) Residue type : (RTA) Atom types : ( C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 C20 O21 O22) Datablock file ? (torsion_rta.dat) Nr of bonds : ( 22)
DIHEDRAL C6 200 C1 200 C2 200 C3 200 -42.76 Skip -> ring torsion
DIHEDRAL C17 200 C1 200 C2 200 C3 200 77.70 Skip -> ring torsion
...
DIHEDRAL C4 200 C5 200 C6 200 C7 200 178.97 Skip -> torsion ~ 180
...
DIHEDRAL C1 200 C6 200 C7 200 C8 200 154.33 Affected atoms : ( C8 C9 C10 C11 C12 C13 C14 C15 C19 C20 O21 O22) OKAY ==> new torsion : (TOR1)
DIHEDRAL C5 200 C6 200 C7 200 C8 200 -32.57 Affected atoms : ( C8 C9 C10 C11 C12 C13 C14 C15 C19 C20 O21 O22) Permutation of : (TOR1) Skip -> permutation
DIHEDRAL C8 200 C7 200 C6 200 C1 200 154.33 Affected atoms : ( C1 C2 C3 C4 C5 C16 C17 C18) OKAY ==> new torsion : (TOR2)
DIHEDRAL C8 200 C7 200 C6 200 C5 200 -32.57 Affected atoms : ( C5 C1 C2 C3 C4 C16 C17 C18) Permutation of : (TOR2) Skip -> permutation
DIHEDRAL C6 200 C7 200 C8 200 C9 200 -179.29 Skip -> torsion ~ 180
...
DIHEDRAL C19 200 C9 200 C8 200 C7 200 -0.57 Skip -> torsion ~ 0
...
DIHEDRAL C13 200 C14 200 C15 200 O21 200 -50.98 Affected atoms : ( O21 O22) OKAY ==> new torsion : (TOR3)
DIHEDRAL C13 200 C14 200 C15 200 O22 200 129.00 Affected atoms : ( O22 O21) Permutation of : (TOR3) Skip -> permutation
DIHEDRAL O21 200 C15 200 C14 200 C13 200 -50.98 Affected atoms : ( C13 C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C16 C17 C18 C19 C20) Skip -> too many affected atoms
DIHEDRAL O22 200 C15 200 C14 200 C13 200 129.00 Affected atoms : ( C13 C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C16 C17 C18 C19 C20) Skip -> too many affected atoms
Nr of unique rotatable torsions : ( 3) Nr of lines written : ( 5) Torsion file written (append to torsion.o) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- RESIDUE RTA TORSION TOR1 154. C1 C6 C7 C8 C8 C9 C10 C11 C12 C13 C14 C15 C19 C20 \ O21 O22 TORSION TOR2 154. C8 C7 C6 C1 C1 C2 C3 C4 C5 C16 C17 C18 TORSION TOR3 -51. C13 C14 C15 O21 O21 O22 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
unix > cp odat/torsion.o .
unix > cat torsion.o torsion_rta.dat torsion_gsb.dat > q
unix > mv q torsion.o
unix > wc torsion.o
139 1381 5430 torsion.o
unix > vi torsion.o
{ change nr of lines in datablock from 100 to 139 - 1 = 138 }
unix > ono test.o
...
O > read torsion.o
O > tor_res hc2 200
Mnp> HC2 200 CA RTA
O > yes
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (RSFIt) Which residue number ? ( 7) 2001092 C1 RTA 200 21.972 29.831 16.739 1.00 15.25 6 1093 C2 RTA 200 20.921 30.524 15.841 1.00 15.61 6 ... 1113 O22 RTA 200 21.840 21.712 27.037 1.00 10.99 8
Nr of atoms found : ( 22) Residue type : (RTA) Atom types : ( C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 C20 O21 O22) Datablock file ? (rsfit_rta.odb) Datablock name : (rsfit_RTA) Datablock written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ! Created by MOLEMAN V. 950417/5.9.5 at Mon Apr 17 23:03:24 1995 for user gerard ! ! RS-fit datablock for RTA ! rsfit_RTA T 2 70 C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C12 C13 C14 C15 C16 C17 C18 C19 C20 O21 O22 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ_pdb_file) disuName of disulfide ODL file ? (ss.odl) Name of the molecule in O ? (M1) cbh1 Stick radius (A) ? ( 0.200) Max SS bond length (A) ? ( 2.500)
25 SG CYS A 4 36.618 67.989 34.228 1.00 21.90 16 148 SG CYS A 19 46.720 75.194 72.769 1.00 16.00 16 181 SG CYS A 25 47.360 76.947 73.550 1.00 18.46 16 375 SG CYS A 50 30.049 62.231 34.042 1.00 18.22 16 ... 2471 SG CYS A 331 31.545 52.779 76.335 1.00 14.21 16 2964 SG CYS A 397 13.725 68.319 69.507 1.00 13.82 16
Nr of CYS SG atoms found : ( 20)
S=S bond : (stick cbh1 a4 sg cbh1 a72 sg 0.20) SG-SG distance (A) : ( 2.030) S=S bond : (stick cbh1 a19 sg cbh1 a25 sg 0.20) SG-SG distance (A) : ( 2.023) ... S=S bond : (stick cbh1 a261 sg cbh1 a331 sg 0.20) SG-SG distance (A) : ( 2.034)
Nr of disulfide bridges : ( 10) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- begin ssbond colour green stick cbh1 a4 sg cbh1 a72 sg 0.20 stick cbh1 a19 sg cbh1 a25 sg 0.20 stick cbh1 a50 sg cbh1 a71 sg 0.20 stick cbh1 a61 sg cbh1 a67 sg 0.20 stick cbh1 a138 sg cbh1 a397 sg 0.20 stick cbh1 a172 sg cbh1 a210 sg 0.20 stick cbh1 a176 sg cbh1 a209 sg 0.20 stick cbh1 a230 sg cbh1 a256 sg 0.20 stick cbh1 a238 sg cbh1 a243 sg 0.20 stick cbh1 a261 sg cbh1 a331 sg 0.20 end_object ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This command generates an O macro which for each water will calculate the RS-fit value and use RSR_rigid to adjust its position in the density. Afterwards, RS-fit is calculated again.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ_pdb_file) fit_wName of water-fitting O macro ? (fit_waters.omac) O macro written Nr of waters to be fitted : ( 486) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
NOTE: you *must* have the appropriate RS-fit datablock in your database. For instance, if you call your waters HOH and the oxygen atoms O1, then you must have the following datablock:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- RSFIT_HOH T 1 70 O1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The macro may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
! Created by MOLEMAN V. 950311/5.9 at Sat Mar 11 21:04:40 1995 for user gerard
!
bell Message Set up for water fitting ...
!
symbol mymol # Molecule name ? #
mol $mymol
!
symbol mymap # Map file name ? #
map_file $mymap
rsr_map $mymap
!
rsr_setup
yes
no
conv
# RS-fit RFAC or RSCC ? #
yes
;
;
20.0
3.5
;
3
10.0
!
bell Message Fitting waters of mol $mymol in map $mymap ...
!
rs_fit C600 ;
rsr_rigid C600 ; yes
!
rs_fit C601 ;
rsr_rigid C601 ; yes
...
rs_fit M957 ;
rsr_rigid M957 ; yes
!
Message Calculating new RS-fit values
! copy_db ${mymol}//_residue_rsprefit ${mymol}//_residue_rsfit
rs_fit C600 M957
!
on_off bell Message Done
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Suppose you want to colour your molecule according to the colours of
your national flag ;-) This command creates an _ATOM_FLAG datablock
with integer values for each atom that encode which colour it should
get in the flag-colouring scheme.
At present, only two types of flag are implemented:
- "Dutch type" - three horizontal or vertical bars (good for the
Dutch, Italian, Belgian, German, French flags)
- "Swedish type" - also good for Denmark, Norway and Finland
The following sketch illustrates the values in the _ATOM_FLAG
datablock:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ------------ ------------ Y-axis | 1 | |1 | | 1 | ^ ------------ ---- ------- | | 2 | | 2 | | ------------ ---- ------- | | 3 | |1 | | 1 | -----------> X-axis ------------ ------------ ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Read the datablock into O and use Paint_case to "translate" these codes into the actual colours of your flag.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ_pdb_file) flag Select one of the following: 1) Dutch/Italian etc. flag colours 2) Swedish/Danish etc. flag colours Which type of flag ? ( 1) Molecule name in O ? (M1) p2a O datablock file ? (p2a_atom_flag.odb) Datablock written; use Paint_case in O ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Now go into O:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- O > mol p2a ce_zo p2a a1 a131 As4> P2A A1 A131 P2A As4> Centering on zone from A1 to A131 O > read p2a_atom_flag.odb O > paint_case Paint> Colour-case a property in molecule P2A Paint> Property [atom_z] : atom_flag Paint> How many cases [8] ? 3 Paint> Enter property values [ 1 2 3] : Paint> Enter 3 colour names: Paint> Colour? [yellow]: red white blue O > zo ; end ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that you must look along the Z-axis.
For a Swedish-type flag use:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- O > mol cbh1 ce_zo cbh1 a1 a434 As4> CBH1 A1 A434 CBH1 As4> Centering on zone from A1 to A434 O > read cbh1_atom_flag.odb O > pa_case atom_flag 2 ; blue yellow O > zo ; end ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (PIR_) stat Nr of atom numbers in memory : ( 7038)Item Average St.Dev Min Max ---- ------- ------ --- --- X-coord 10.543 22.100 -33.949 54.913 Y-coord 42.379 23.814 -2.748 86.626 Z-coord 33.375 31.576 -29.766 91.680 B-factor 17.965 8.663 5.310 67.750 Occpncy 1.000 0.000 1.000 1.000
Radius of gyration (A) : 45.31 Sum of masses : 95666.758 Centre-of-mass : 10.54 42.31 33.37 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Make 2D plot file for O2D with CA-CA distance matrix; plot and convert to PostScript with O2D
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (B_Q_) ca_dName for C-alpha distance plot file ? (Calpha.pl2) ca_ca_1rbp.plt Nr of C-alpha atoms : ( 174) Nr of points written : ( 30276) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- unix > run o2d Option ? (open_window) open 2 1 0 1 Option ? (open_window 2 1 0) 2d ca_ca_1rbp.plt ca_ca_1rbp.ps ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ_pdb_file) plotMake plot file for Bs or Qs ? (B) Filename for per_atom plot ? (atom_b.plt) hc2_atomb.plt Filename for per_residue plot ? (resi_b.plt) hc2_rmsb.plt
You may plot the following for each residue: R = RMS B/Q for all atoms in the residue A = average B/Q for all atoms M = average B/Q for main-chain atoms S = average B/Q for side-chain atoms Option (R/A/M/S) ? (A) r Write atom/residue labels to file (Y/N) ? (N) WARNING - if there are hydrogen atoms they will be included ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Make an O2D plot file of the radial distribution of temperature factors. The Bs are averaged for 2 A shells of distance to the centre-of-gravity. A normal protein should have the lowest Bs for the core, and increasingly higher Bs further away.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ_pdb_file) radi Plot file ? (b_radial.plt) cbh1_brad.plt Which chain (2 characters !) ? ( A) Nr of atoms selected (no Hs) : ( 3220) Shell 0.0 - 2.0 A - 3 atoms; <B> = 13.80 A**2 Shell 2.0 - 4.0 A - 6 atoms; <B> = 13.06 A**2 Shell 4.0 - 6.0 A - 36 atoms; <B> = 11.43 A**2 Shell 6.0 - 8.0 A - 62 atoms; <B> = 11.84 A**2 Shell 8.0 - 10.0 A - 102 atoms; <B> = 12.34 A**2 Shell 10.0 - 12.0 A - 143 atoms; <B> = 12.89 A**2 Shell 12.0 - 14.0 A - 193 atoms; <B> = 13.60 A**2 Shell 14.0 - 16.0 A - 289 atoms; <B> = 14.66 A**2 Shell 16.0 - 18.0 A - 364 atoms; <B> = 15.69 A**2 Shell 18.0 - 20.0 A - 449 atoms; <B> = 16.49 A**2 Shell 20.0 - 22.0 A - 417 atoms; <B> = 18.10 A**2 Shell 22.0 - 24.0 A - 406 atoms; <B> = 19.59 A**2 Shell 24.0 - 26.0 A - 315 atoms; <B> = 21.47 A**2 Shell 26.0 - 28.0 A - 200 atoms; <B> = 24.85 A**2 Shell 28.0 - 30.0 A - 118 atoms; <B> = 24.41 A**2 Shell 30.0 - 32.0 A - 81 atoms; <B> = 27.30 A**2 Shell 32.0 - 34.0 A - 27 atoms; <B> = 24.15 A**2 Shell 34.0 - 36.0 A - 9 atoms; <B> = 37.11 A**2 Plot file written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (STAT) list Which residue number ? ( 1) 134 998 N SER A 134 22.506 77.869 68.784 1.00 10.34 1CEL1371 999 CA SER A 134 21.237 78.577 68.983 1.00 12.57 1CEL1372 1000 C SER A 134 20.246 78.558 67.822 1.00 14.46 1CEL1373 1001 O SER A 134 19.033 78.613 68.042 1.00 15.10 1CEL1374 1002 CB SER A 134 21.467 80.023 69.448 1.00 10.64 1CEL1375 1003 OG SER A 134 22.059 80.811 68.438 1.00 14.16 1CEL1376 4516 N SER B 134 -16.718 34.527 12.931 1.00 10.28 1CEL4890 4517 CA SER B 134 -17.987 35.226 13.120 1.00 13.83 1CEL4891 4518 C SER B 134 -18.962 35.238 11.945 1.00 14.82 1CEL4892 4519 O SER B 134 -20.173 35.316 12.154 1.00 15.94 1CEL4893 4520 CB SER B 134 -17.753 36.658 13.617 1.00 12.94 1CEL4894 4521 OG SER B 134 -17.244 37.491 12.594 1.00 14.21 1CEL4895 Nr of atoms listed : ( 12) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
(1) of a residue: list all distances, all bond angles
and all 1-4-dihedral angles (NOTE: if you use a
VERY large number for the cut-off distance for
bonded atoms you will get ALL angles and dihedrals)
(2) of the N-CA-C backbone; listed are the names of the
atoms, the distance to the previous atom, the
bond angle involving the two preious atoms and the
1-4-dihedral angle involving the three previous atoms
(3) of the CA backbone: same output as for (2)
(4) of two residues (neighbours or disulfides)
(5) of a zone of residues
(6) of a disulfide (limited set of bonds, angles and
dihedrals)
With options 1, 4 and 5: if more than 25 atoms are found, only the bonded distances are listed, otherwise the complete distance matrix is printed.
HINT: use this option to find reasonable geometries when you're making dictionary structures for X-PLOR, PROLSQ etc. based for example on a small-molecule structure
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (LIST) geomSelect an option: 1 - analyse one residue 2 - analyse backbone (N-CA-C) 3 - analyse CAs 4 - analyse two residues (eg, disulfide) 5 - analyse zone of residues 6 - analyse disulfide Option (1-6; 0 to abort) ? ( 6) 1 Which residue number ? ( 4) 72 Cut-off distance for bonded atoms ? ( 2.200)
535 N CYS A 72 34.608 63.747 35.816 1.00 17.34 7 536 CA CYS A 72 35.411 64.499 36.779 1.00 17.34 6 537 C CYS A 72 34.530 65.272 37.762 1.00 17.34 6 538 O CYS A 72 33.287 65.334 37.645 1.00 17.34 8 539 CB CYS A 72 36.313 65.488 36.071 1.00 13.02 6 540 SG CYS A 72 35.365 66.531 34.967 1.00 13.02 16
Nr of atoms found : ( 6)
*** Distances *** Complete distance matrix N CA C O CB SG DIST N 0.00 1.46 2.47 2.76 2.45 3.01 DIST CA 1.46 0.00 1.53 2.44 1.51 2.72 DIST C 2.47 1.53 0.00 1.25 2.47 3.18 DIST O 2.76 2.44 1.25 0.00 3.41 3.59 DIST CB 2.45 1.51 2.47 3.41 0.00 1.79 DIST SG 3.01 2.72 3.18 3.59 1.79 0.00
*** Bond angles *** ANGLE N 72 CA 72 C 72 111.52 ANGLE N 72 CA 72 CB 72 110.80 ANGLE C 72 CA 72 CB 72 108.27 ANGLE CA 72 C 72 O 72 122.52 ANGLE CA 72 CB 72 SG 72 110.69
*** Dihedral angles *** DIHEDRAL N 72 CA 72 C 72 O 72 -6.42 DIHEDRAL N 72 CA 72 CB 72 SG 72 53.28 DIHEDRAL C 72 CA 72 CB 72 SG 72 -69.31 DIHEDRAL O 72 C 72 CA 72 CB 72 115.73
Option ? (GEOM) geom
Select an option: 1 - analyse one residue 2 - analyse backbone (N-CA-C) 3 - analyse CAs 4 - analyse two residues (eg, disulfide) 5 - analyse zone of residues 6 - analyse disulfide Option (1-6; 0 to abort) ? ( 1) 6 29 N CYS 4 8.582 27.251 55.048 1.00 25.90 558 N CYS 70 43.922 22.172 50.132 1.00 28.67 964 N CYS 120 19.470 20.072 51.841 1.00 15.63 1032 N CYS 129 14.163 22.087 57.465 1.00 18.90 1283 N CYS 160 14.295 30.222 53.381 1.00 13.24 1402 N CYS 174 44.619 28.164 46.710 1.00 38.08 Nr of CYS/CYH residues : ( 6) First residue number ? ( 160) 120 Second residue number ? ( 174) 129
964 N CYS 120 19.470 20.072 51.841 1.00 15.63 965 CA CYS 120 19.045 19.808 53.200 1.00 17.29 968 CB CYS 120 17.494 19.751 53.374 1.00 15.42 969 SG CYS 120 17.119 19.461 55.134 1.00 15.26 1032 N CYS 129 14.163 22.087 57.465 1.00 18.90 1033 CA CYS 129 15.496 21.513 57.385 1.00 18.30 1036 CB CYS 129 16.160 22.056 56.157 1.00 18.35 1037 SG CYS 129 17.721 21.256 55.804 1.00 15.55
Nr of atoms found : ( 8)
1 2 SG-SG CB-CB CA-CA ===== ===== ===== ===== ===== 120 129 2.01 3.85 5.75
1 2 SG1-SG2-CB2 SG2-SG1-CB1 SG1-CB1-CA1 SG2-CB2-CA2 CB1-CA1-N1 CB2-CA2-N2 ===== ===== =========== =========== =========== =========== =========== =========== 120 129 101.8 96.8 108.5 112.7 113.7 108.0
1 2 N1-CA1-CB1-SG1 CA1-CB1-SG1-SG2 CB1-SG1-SG2-CB2 N2-CA2-CB2-SG2 CA2-CB2-SG2-SG1 ===== ===== =============== =============== =============== =============== =============== 120 129 -178.4 69.4 106.4 -171.8 73.1
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
List peptide improper torsion angles to check for deviations from planarity.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (GEOM) planChecking peptide planarity ... Improper Ci-CAi-Ni+1-Oi should be ZERO degrees The nr of * indicates deviation from planarity
4 O GLU 1 -1.705 *** 13 O ARG 2 -0.389 24 O ASP 3 -2.938 ***** 32 O CYS 4 -1.415 ** ... 1381 O ASN 171 1.228 ** 1389 O GLY 172 0.266 1393 O TYR 173 0.448
Nr of peptide planes : ( 173) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Option ? (BURI) sequ
1 N MET A 1 11.840 26.637 68.001 1.00 40.61 1CHR 160
9 N LYS A 2 11.559 28.870 65.489 1.00 38.38 1CHR 168
...
5589 N VAL B 369 2.619 61.125 63.785 1.00 44.83 1CHR5749
5596 N SER B 370 4.907 58.580 62.590 1.00 44.48 1CHR5756
5603 MN MN B 371 26.234 61.708 57.860 1.00 23.51 1CHR5764
Nr of residues found : ( 743)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Assess how well charged protein residues are surrounded
by counter-charged residues, N/O/S etc. (using a
distance cut-off of 3.5 A). Solvent-exposed residues are
"recognised" by their having a small number of neighbours.
Note that the program only knows something about charges of
hetero atoms if the atom name contains a "+" or "-" sign (e.g.,
"CA++" will be recognised as a positively charged atom).
This option can be used to find buried charges, which may indicate
errors in the tracing of the chain. For example, using PDB file 1CHR
(in which residues 15-40 are out-of-register in both chains):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ) buri ... ==> GLU - 7 Neighbours for OE1 ... ... VAL - 34 - CB @ 3.43 A ... VAL - 34 - CG1 @ 3.21 A ... VAL - 36 - CB @ 3.05 A ... VAL - 36 - CG2 @ 3.11 A Neighbours for OE2 ... ... VAL - 36 - CB @ 3.46 A ... VAL - 36 - CG2 @ 3.47 A #C 6 | #N 0 | #O 0 | #S 0 | #other 0 #water 0 | #positive 0 | #negative 0 | #total 6 > Appears not to be solvent exposed > No positive charge(s) nearby !! > Not many nitrogens nearby !! > Not many waters nearby !! > Many C/S nearby !! ... ==> ARG - 17 Neighbours for NE ... Neighbours for NH1 ... Neighbours for NH2 ... ... ILE - 19 - CG1 @ 3.26 A ... ILE - 19 - CD1 @ 3.05 A ... LYS - 165 - CE @ 3.29 A ... LYS - 165 - NZ @ 3.36 A #C 3 | #N 1 | #O 0 | #S 0 | #other 0 #water 0 | #positive 1 | #negative 0 | #total 4 > Appears not to be solvent exposed > Positive charge(s) nearby !! > No negative charge(s) nearby !! > Not many O/S nearby !! > Many carbons nearby !! ... ==> ARG - 35 Neighbours for NE ... ... TYR - 37 - CE1 @ 3.45 A ... LEU - 108 - CA @ 3.31 A ... LEU - 108 - CD2 @ 3.30 A Neighbours for NH1 ... ... ILE - 3 - CD1 @ 3.07 A ... ALA - 80 - CA @ 3.33 A ... ALA - 80 - CB @ 3.41 A ... LEU - 108 - CG @ 3.37 A ... LEU - 108 - CD1 @ 2.91 A ... LEU - 108 - CD2 @ 3.13 A Neighbours for NH2 ... ... ALA - 80 - CA @ 3.27 A ... ALA - 80 - C @ 3.42 A ... ALA - 80 - O @ 2.89 A ... ALA - 80 - CB @ 3.38 A ... LEU - 108 - CA @ 2.94 A ... LEU - 108 - C @ 3.40 A ... LEU - 108 - O @ 3.08 A ... LEU - 108 - CB @ 3.03 A ... LEU - 108 - CD1 @ 3.38 A #C 16 | #N 0 | #O 2 | #S 0 | #other 0 #water 0 | #positive 0 | #negative 0 | #total 18 > Appears not to be solvent exposed > No negative charge(s) nearby !! > Not many O/S nearby !! > Many carbons nearby !! ... ==> GLU - 39 Neighbours for OE1 ... ... LEU - 41 - O @ 2.63 A ... LEU - 111 - CD2 @ 3.24 A Neighbours for OE2 ... ... TYR - 37 - CD2 @ 3.12 A ... TYR - 37 - CE2 @ 3.33 A ... SER - 38 - N @ 3.07 A ... SER - 38 - C @ 3.33 A #C 4 | #N 1 | #O 1 | #S 0 | #other 0 #water 0 | #positive 0 | #negative 0 | #total 6 > Appears not to be solvent exposed > No positive charge(s) nearby !! > Not many nitrogens nearby !! > Not many waters nearby !! > Many C/S nearby !! ... ==> LYS - 64 Neighbours for NZ ... ... GLU - 68 - OE2 @ 3.00 A ... ARG - 368 - NH2 @ 3.35 A #C 0 | #N 1 | #O 1 | #S 0 | #other 0 #water 0 | #positive 1 | #negative 1 | #total 2 > Appears to be solvent exposed ... ==> GLU - 220 Neighbours for OE1 ... ... ASP - 194 - CG @ 2.99 A ... ASP - 194 - OD1 @ 2.73 A ... ASP - 194 - OD2 @ 2.71 A ... ASP - 245 - CB @ 3.45 A ... ASP - 245 - CG @ 3.46 A ... ASP - 245 - OD2 @ 2.71 A ... GLU - 246 - OE1 @ 2.81 A ... MN - 371 - MN @ 3.50 A Neighbours for OE2 ... ... ASP - 194 - OD2 @ 3.00 A ... ASP - 245 - OD2 @ 2.88 A ... MN - 371 - MN @ 2.72 A #C 3 | #N 0 | #O 6 | #S 0 | #other 2 #water 0 | #positive 0 | #negative 6 | #total 11 > Appears not to be solvent exposed > Negative charge(s) nearby !! > No positive charge(s) nearby !! > Not many nitrogens nearby !! > Not many waters nearby !! > Many C/S nearby !! ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Hydrogen atoms are ignored. Short distances involving atoms in I-1,I,I+1
residues are ignroed, unless they are shorter than 1.1 A (MOLEMAN doesn't
know anything about connectivity).
From version 7.0 onwards, REMARK records are added with some of the
results of this operation (don't forget to WRITe the structure in
order to get these REMARKs included in your PDB file). This may be
useful when depositing coordinates with the PDB.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (REMA) shor Cut-off distance for SHORT contacts ? ( 2.400) Short contacts : ( 0) Any hydrogen atoms have been ignored Short contacts between I-1,I,I+1 residues ignored (unless they are shorter than 1.1 A) Generating REMARK records ... CPU total/user/sys : 1.6 1.5 0.0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The REMARK records may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (CA_R) rema # 1 > HEADER RETINOIC-ACID TRANSPORT 28-SEP-94 1CBS 1CBS 2 ... #277 > REMARK 5 SHORT CONTACTS (EXCL. HYDROGENS AND SYMMETRY) #278 > REMARK 5 PROGRAM USED: MOLEMAN #279 > REMARK 5 NUMBER OF SHORT CONTACTS : 0 #280 > REMARK 5 DISTANCE CUTOFF (A) : 2.40 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Calculate all inter-atomic distances between non-hydrogen atoms, and list the results as a histogram. This can be used to decide on reasonable Patterson integration limits for rotation function calculations, in particular for molecules which have a non-spherical shape.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Option ? (READ_pdb_file) dist
Counting distances (Hs ignored) ...
Nr of non-hydrogen atoms : ( 3220)
Nr of inter-atomic distances : ( 5182590)
Lower(A) Upper(A) Count % Cumul Cumul%
1.00 1.50 2040 0.039 2040 0.039
1.50 2.00 1256 0.024 3296 0.064
2.00 2.50 3601 0.069 6897 0.133
2.50 3.00 2650 0.051 9547 0.184
3.00 3.50 3508 0.068 13055 0.252
3.50 4.00 6508 0.126 19563 0.377
4.00 4.50 7682 0.148 27245 0.526
4.50 5.00 11756 0.227 39001 0.753
...
40.00 40.50 44819 0.865 4607902 88.911
40.50 41.00 42217 0.815 4650119 89.726
41.00 41.50 40038 0.773 4690157 90.498
41.50 42.00 38019 0.734 4728176 91.232
42.00 42.50 35695 0.689 4763871 91.921
...
66.00 66.50 4 0.000 5182579 100.000
66.50 67.00 9 0.000 5182588 100.000
67.00 67.50 2 0.000 5182590 100.000
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Option ? (READ_pdb_file) chi_
Residue CHI1 CHI2 CHI3 CHI4
PYR 1 29.44 -25.85 -163.81
SER 2 67.11
ALA 3
CYS 4 -80.06
THR 5 49.97
LEU 6 -62.38 -169.53
GLN 7 153.17 62.98 -106.58
SER 8 51.40
...
TRP 16 57.07 -80.75
GLN 17 -63.54 -83.16 -35.11
LYS 18 -179.84 172.97 -176.26 124.61
CYS 19 -52.68
SER 20 65.99
...
ASN 431 -69.14 -31.87
PRO 432 -34.48 45.26
SER 433 -61.22
GLY 434
Option ? (CHI_)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
List statistics about CA-CA distances. There are five intervals:
- short : d <= 2.8 A -> expected = 0.01 % (0.08) of the residues
- cis : 2.8 < d <= 3.0 A -> expected = 0.24 % (0.46) of the residues
- poor : 3.0 < d <= 3.7 A -> expected = 1.52 % (3.5) of the residues
- trans : 3.7 < d <= 3.9 A -> expected = 96.8 % (7.0) of the residues
- long : 3.9 < d -> expected = 1.42 % (4.0) of the residues
If there are many short, poor or long CA-CA distances, the model is
probably un/ill-refined.
From version 7.0 onwards, REMARK records are added with some of the
results of this operation (don't forget to WRITe the structure in
order to get these REMARKs included in your PDB file). This may be
useful when depositing coordinates with the PDB.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Option ? (READ) caca
136 CA-CA distances
Average CA-CA distance = 3.807 Sigma = 0.018
Minimum CA-CA distance = 3.764 Maxim = 3.857
Short (<= 2.8 A) CA-CA dists : 0 res = 0.00 % = 0.1 SIGMA from mean
CIS (<= 3.0 A) CA-CA dists : 0 res = 0.00 % = 0.5 SIGMA from mean
Poor (<= 3.7 A) CA-CA dists : 0 res = 0.00 % = 0.4 SIGMA from mean
TRANS (<= 3.9 A) CA-CA dists : 136 res = 100.00 % = 0.5 SIGMA from mean
Long (> 3.9 A) CA-CA dists : 0 res = 0.00 % = 0.4 SIGMA from mean
Generating REMARK records ...
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The REMARK records may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (CA_R) rema # 1 > HEADER RETINOIC-ACID TRANSPORT 28-SEP-94 1CBS 1CBS 2 ... #216 > REMARK 5 CA-CA DISTANCE DISTRIBUTION #217 > REMARK 5 PROGRAM USED: MOLEMAN #218 > REMARK 5 NUMBER OF DISTANCES : 136 #219 > REMARK 5 SHORT (<= 2.8 A) (NR) : 0 #220 > REMARK 5 SHORT (<= 2.8 A) (%) : 0.00 #221 > REMARK 5 CIS (2.8 - 3.0 A) (NR) : 0 #222 > REMARK 5 CIS (2.8 - 3.0 A) (%) : 0.00 #223 > REMARK 5 POOR (3.0 - 3.7 A) (NR) : 0 #224 > REMARK 5 POOR (3.0 - 3.7 A) (%) : 0.00 #225 > REMARK 5 TRANS (3.7 - 3.9 A) (NR) : 136 #226 > REMARK 5 TRANS (3.7 - 3.9 A) (%) : 100.00 #227 > REMARK 5 LONG (> 3.9 A) (NR) : 0 #228 > REMARK 5 LONG (> 3.9 A) (%) : 0.00 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Calculate CA-CA(*)-CA angles and CA-CA(*)-CA-CA dihedrals for
the CA atoms (marked with an asterisk).
Residues in an alpha-helix should cluster tightly around ~(90,50);
beta-strands occur around ~(120,-160) with somewhat more spread.
If you ask for a PostScript file, you get the most favoured
regions in green, the additional favoured regions in blue, and
the border of the disallowed regions in red. Glycines will be
marked with a small box, all other residues with a plus sign.
The regions are based on an analysis of 203,865 non-Gly residues
in less than 90 % homologous proteins from the PDB (Hobohm & Sander
list, October 1994).
The statistics are based on how 1,343 2.0 A or better structures
score on the four assigned regions. Too few core, or too many
disallowed residues indicates an un/ill-refined model and/or
a problem with the fold.
From version 7.0 onwards, REMARK records are added with some of the
results of this operation (don't forget to WRITe the structure in
order to get these REMARKs included in your PDB file). This may be
useful when depositing coordinates with the PDB.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (REMA) ca_r Initialising CA_Ramachandran pixels ... Pixels with value 0,1,2,3 : ( 5359 1110 387 525)In the following, hit RETURN if you do NOT want to produce the file the programs asks for
Text file with CA angles/dihedrals ? ( ) O2D CA angles/dihedrals plot file ? ( ) PostScript CA angles/dihedrals plot file ? ( ) q.ps => XPS_GRAF - GJK (2.2 @ 950530) Opened PostScript file : (q.ps) Date : (Mon Oct 30 22:17:02 1995) User : (gerard) Program : (MOLEMAN) Nr of non-GLY residues : ( 126) CORE res : 92 = 73.02 % = 0.0 SIGMA from mean Additional res : 17 = 13.49 % Generous res : 10 = 7.94 % DISALLOWED res : 7 = 5.56 % = 1.1 SIGMA from mean For <= 2.0 A structures : Core - 7.1 % area - 72.8 % (8.9) residues Additional - 5.2 % area - 12.8 % (4.0) residues Generous - 15.0 % area - 11.3 % (4.6) residues Disallowed - 72.6 % area - 3.1 % (2.2) residues Generating REMARK records ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The REMARK records may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (CA_R) rema # 1 > HEADER RETINOIC-ACID TRANSPORT 28-SEP-94 1CBS 1CBS 2 ... #230 > REMARK 5 CA RAMACHANDRAN PLOT #231 > REMARK 5 PROGRAM USED: MOLEMAN #232 > REMARK 5 NUMBER OF RESIDUES : 126 #233 > REMARK 5 CORE REGIONS (NR) : 92 #234 > REMARK 5 CORE REGIONS (%) : 73.02 #235 > REMARK 5 ADDITIONAL REGIONS (NR) : 17 #236 > REMARK 5 ADDITIONAL REGIONS (%) : 13.49 #237 > REMARK 5 GENEROUS REGIONS (NR) : 10 #238 > REMARK 5 GENEROUS REGIONS (%) : 7.94 #239 > REMARK 5 DISALLOWED REGIONS (NR) : 7 #240 > REMARK 5 DISALLOWED REGIONS (%) : 5.56 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
These options make MOLEMAN calculate the PHI and PSI angles for those residues that contain atoms called ' N ', ' CA ' and ' C '. You may obtain output in several formats:
(1) a text file with PHI-PSI values
(2) a plot file for use with O2D (RAMA only !)
(3) an "O" datablock file (use with OOPS !!)
(4) a plot file in HPGL format (use "print_hpgl" on XRAY)
(5) a plot file in PostScript format (use "lpr -Pqms")
MOLEMAN asks you for the names of ALL these files; if you do
not want a particular one, don't give a file name (i.e., just
hit RETURN when the program asks you for the file name).
These options make the standalone programs RAMACH and RAMAPS
obsolete; they provide a superset of the functionality of
these two programs.
Note that in Balasubramanian plots GLY residues are plotted
with a little square (just as in Ramachandran plots) so you
can recognise them easily !
These options use some of Alwyn's old RAMACH code.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (CA_Rama) ramaIn the following, hit RETURN if you do NOT want to produce the file the programs asks for
Text file with PHI-PSIs ? ( ) O2D Ramachandran plot file ? ( ) O PHI-PSI datablock file ? ( ) HPGL Ramachandran plot file ? ( ) PostScript Ramachandran plot file ? ( ) cbh1_rama.ps => XPS_GRAF - GJK (2.2 @ 950530) Opened PostScript file : (cbh1_rama.ps) Date : (Wed Oct 11 01:48:29 1995) User : (gerard) Program : (MOLEMAN) PostScript POLAR Ramachandran plot file ? ( ) Option ? (RAMA) bala
In the following, hit RETURN if you do NOT want to produce the file the programs asks for
Text file with PHI-PSIs ? ( ) O PHI-PSI datablock file ? ( ) HPGL Balasubramanian plot file ? ( ) PostScript Balasubramanian plot file ? ( ) cbh1_bala.ps => XPS_GRAF - GJK (2.2 @ 950530) Opened PostScript file : (cbh1_bala.ps) Date : (Wed Oct 11 01:48:44 1995) User : (gerard) Program : (MOLEMAN) Label for residue axis ? (Residue) Label for PHI-PSI axis ? (PHI/PSI) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
From version 7.2 onward, (ONLY) when you select a PostScript file, you get improved allowed regions and some statistics. One would expect ~2% outliers using this definition (see the example).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- PostScript Ramachandran plot file ? ( ) cbh1_rama.ps => XPS_GRAF - GJK (2.3 @ 960209) Opened PostScript file : (cbh1_rama.ps) Date : (Fri Feb 9 22:22:45 1996) User : (gerard) Program : (MOLEMAN) Nr of non-Gly residues : ( 764) Nr of outliers (98%) : ( 5) % Outliers : ( 0.654) Outliers are defined as residues lying outside the core areas in which 98% of all non-Gly residues were found to lie in a sample of 403 PDB structures of <= 95% homologous structures (Hobohm & Sander list) at 2.0 A resolution or better (GJK, October 1995, unpublished results; data for 74,893 residues). Outliers are shown as asterisks in the plot; core areas are coloured grey. ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (BALA) temp TFnew = A * TFold + B. Enter A, B : ( 1.000 0.000) 0 15.0 Residue range to apply (0 0 = all molecule) ? ( 0 0) Nr of temperature factors updated : ( 7038) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ) aver Valid options are: 1. Average over all atoms (i.e., compute Boverall) 2. Average per residue over all atoms 3. Average per residue, separately for main and side-chain 4. Average corresponding atoms in different chainsOption ? ( 3) Res 1 Nr_atoms 7 Bave-MC 28.08 ( 4) Bave-SC 29.75 ( 3) Res 2 Nr_atoms 8 Bave-MC 19.20 ( 4) Bave-SC 24.23 ( 4) Res 3 Nr_atoms 11 Bave-MC 12.96 ( 4) Bave-SC 11.13 ( 7) Res 4 Nr_atoms 6 Bave-MC 10.79 ( 4) Bave-SC 15.15 ( 2) ... Res 398 Nr_atoms 1 Bave-MC 39.26 ( 1) Bave-SC 0.00 ( 0) Res 399 Nr_atoms 1 Bave-MC 33.87 ( 1) Bave-SC 0.00 ( 0) Nr of temperature factors updated : ( 1213) Option ? (AVER) Valid options are: 1. Average over all atoms (i.e., compute Boverall) 2. Average per residue over all atoms 3. Average per residue, separately for main and side-chain 4. Average corresponding atoms in different chains
Option ? ( 3) 1 Nr of temperature factors updated : ( 1213) Average temperature factor : ( 16.622) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (AVER) occu OFnew = A * OFold + B. Enter A, B : ( 1.000 0.000) 0 1.0 Residue range to apply (0 0 = all molecule) ? ( 0 0) Nr of occupancy factors updated : ( 1213) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (XPLOr) occu OFnew = A * OFold + B. Enter A, B : ( 1.000 0.000) 0 0 Residue range to apply (0 0 = all molecule) ? ( 1 138) 76 82 Nr of occupancy factors updated : ( 36) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (AUTO) b_q_ Amino acid residue names ? (ALA ARG ASN ASP CYS GLN GLU GLY HIS ILE LEU LYS MET PHE PRO SER THR TRP TYR VAL CPR ASX GLX UNK CYH CSS PCA) Names of ligands/substrates ? (???) Which chain (** = all) ? ( A) Include HYDROGEN atoms (Y/N) ? (N)B & Q statistics for chain : ( A)
Atom type Number Average B Maximum B Average Q Protein main chain 549 12.925 37.810 1.000 Protein side chain 542 18.069 53.120 1.000 Protein all atoms 1091 15.480 53.120 1.000 Ligand/substrate 0 0.000 0.000 0.000 Water molecules 0 0.000 0.000 0.000 Other entities 0 0.000 0.000 0.000 All atoms 1091 15.480 53.120 1.000 Generating REMARK records ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The REMARK records may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (CA_R) rema # 1 > HEADER RETINOIC-ACID TRANSPORT 28-SEP-94 1CBS 1CBS 2 ... #282 > REMARK 5 B-FACTOR STATISTICS FOR CHAIN A (EXCL. HYDROGENS) #283 > REMARK 5 PROGRAM USED: MOLEMAN #284 > REMARK 5 PROTEIN MAIN CHAIN #285 > REMARK 5 NUMBER OF ATOMS : 549 #286 > REMARK 5 AVERAGE B (A**2) : 12.92 #287 > REMARK 5 MAXIMUM B (A**2) : 37.81 #288 > REMARK 5 PROTEIN SIDE CHAIN #289 > REMARK 5 NUMBER OF ATOMS : 542 #290 > REMARK 5 AVERAGE B (A**2) : 18.07 #291 > REMARK 5 MAXIMUM B (A**2) : 53.12 #292 > REMARK 5 PROTEIN ALL ATOMS #293 > REMARK 5 NUMBER OF ATOMS : 1091 #294 > REMARK 5 AVERAGE B (A**2) : 15.48 #295 > REMARK 5 MAXIMUM B (A**2) : 53.12 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Calculate RMSD and correlation coefficient of the temperature
factors of bonded atoms (plus a warning if the RMSD is large)
From version 7.0 onwards, REMARK records are added with some of the
results of this operation (don't forget to WRITe the structure in
order to get these REMARKs included in your PDB file). This may be
useful when depositing coordinates with the PDB.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (REMA) bond Cut-off distance for bonded atoms ? ( 2.000) 1.8Nr of atoms : ( 1213) Nr of non-Hs : ( 1213) Nr of bonds : ( 1124) RMSD bonded Bs : ( 2.200) Corr. coeff. : ( 0.970) Hydrogen atoms have been ignored Ignore the following line in case of grouped Bs Bonded Bs properly restrained Generating REMARK records ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The REMARK records may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (CA_R) rema # 1 > HEADER RETINOIC-ACID TRANSPORT 28-SEP-94 1CBS 1CBS 2 ... #242 > REMARK 5 BONDED B-FACTORS (EXCL. HYDROGENS) #243 > REMARK 5 PROGRAM USED: MOLEMAN #244 > REMARK 5 NUMBER OF NON-H ATOMS : 1213 #245 > REMARK 5 BOND DISTANCE CUTOFF (A) : 1.80 #246 > REMARK 5 NUMBER OF BONDS : 1124 #247 > REMARK 5 RMSD B-BONDED (A**2) : 2.20 #248 > REMARK 5 CORR. COEFF. B-BONDED : 0.97 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Calculate RMSD and correlation coefficient of the temperature
factors of NON-bonded atoms
From version 7.0 onwards, REMARK records are added with some of the
results of this operation (don't forget to WRITe the structure in
order to get these REMARKs included in your PDB file). This may be
useful when depositing coordinates with the PDB.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (REMA) nonb RMS delta-B of non-bonded atoms Select one of the following options : 1 = all atoms 2 = N and O only (H-bonds & salt links) 3 = all atoms, except N and O Option (1-3) ? ( 1) Cut-off distance for bonded atoms ? ( 1.800) Cut-off for NON-bonded atoms ? ( 3.600)Number of atoms : ( 1213) Number of atoms used : ( 1213) Nr of non-bonded contacts : ( 3765) RMSD non-bonded Bs : ( 6.125) Correlation coefficient : ( 0.725) Hydrogen atoms have been ignored Generating REMARK records ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The REMARK records may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (CA_R) rema # 1 > HEADER RETINOIC-ACID TRANSPORT 28-SEP-94 1CBS 1CBS 2 ... #250 > REMARK 5 NON-BONDED B-FACTORS (EXCL. HYDROGENS) #251 > REMARK 5 PROGRAM USED: MOLEMAN #252 > REMARK 5 NUMBER OF NON-H ATOMS : 1213 #253 > REMARK 5 BOND DISTANCE CUTOFF (A) : 1.80 #254 > REMARK 5 NON-BONDED CUTOFF (A) : 3.60 #255 > REMARK 5 NUMBER OF INTERACTIONS : 3765 #256 > REMARK 5 RMSD B-NON-BONDED (A**2) : 6.12 #257 > REMARK 5 CORR. COEFF. B-BONDED : 0.73 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
When you want to change from refining grouped temperature
factors to individual Bs, or when the RMS delta-B of
bonded atoms is too large, you can use this command to
replace every atom's B-factor by the average B of all
its bonded neighbours including itself.
In order to include second neighbours or even non-bonded
neighbours, use an artificially large cut-off
for bonded atoms, e.g. 2.5 - 3.5 A.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ_pdb_file) bond Cut-off distance for bonded atoms ? ( 2.000) ... RMSD bonded Bs : ( 6.085) Corr. coeff. : ( 0.912) ... Option ? (BOND) smoo Cut-off distance for bonded atoms ? ( 2.000) Smoothing temperature factors ...Nr of atoms : ( 3338) Nr of non-Hs : ( 2747) Nr of bonds : ( 2823) Hydrogen atoms have been ignored Option ? (SMOO) bond ... RMSD bonded Bs : ( 3.760) ... Option ? (BOND) smoo Cut-off distance for bonded atoms ? ( 2.000) Smoothing temperature factors ...
Nr of atoms : ( 3338) Nr of non-Hs : ( 2747) Nr of bonds : ( 2823) Hydrogen atoms have been ignored Option ? (SMOO) bond ... RMSD bonded Bs : ( 3.153) ... Option ? (BOND) smoo ... Option ? (SMOO) bond ... RMSD bonded Bs : ( 2.833) Corr. coeff. : ( 0.978) ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ) bond Cut-off distance for bonded atoms ? ( 2.000) 3.5Nr of atoms : ( 3338) Nr of non-Hs : ( 2747) Nr of bonds : ( 10909) RMSD bonded Bs : ( 9.505) Corr. coeff. : ( 0.737) Hydrogen atoms have been ignored Ignore the following line in case of grouped Bs Use stronger restraints on bonded Bs Option ? (BOND) smoo Cut-off distance for bonded atoms ? ( 3.500) Smoothing temperature factors ...
Nr of atoms : ( 3338) Nr of non-Hs : ( 2747) Nr of bonds : ( 10909) Hydrogen atoms have been ignored Option ? (SMOO) bond ... RMSD bonded Bs : ( 4.487) ... Option ? (BOND) smoo Cut-off distance for bonded atoms ? ( 3.500) ... Option ? (SMOO) bond Cut-off distance for bonded atoms ? ( 3.500) ... RMSD bonded Bs : ( 3.299) ... Option ? (BOND) smoo Cut-off distance for bonded atoms ? ( 3.500) ... Option ? (SMOO) bond Cut-off distance for bonded atoms ? ( 3.500) ... RMSD bonded Bs : ( 2.655) Corr. coeff. : ( 0.951) ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ) limi Enter MIN and MAX temperature factor : ( 2.000 99.900) 10 50 Enter MIN and MAX occupancy : ( 0.000 1.000) 1 1 Residue range to apply (0 0 = all molecule) ? ( 0 0) Nr of atoms updated : ( 7038) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (OCCU) chai Chain label (2 characters) ? ( ) A Residue range to apply (0 0 = all molecule) ? ( 76 82) 1 138 Nr of chain labels updated : ( 903) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (CHAIn) renum First NEW atom number ? ( 1) Nr of atom numbers updated : ( 1849) Nr of last atom : ( 1849) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Suggest reasonable coordinates for C-terminal OT1 and OT2 oxygens (required by X-PLOR) using standard geometries
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (WATEr) sugg Which residue number ? ( 120) 174 ... found N ... found CA ... found C ... found O Using C-OT distance (A) : ( 1.230) Using OT-C-OT angle (deg) : ( 122.500) Distance C-OT1 = ( 1.241) Reset to = ( 1.230) Angle CA-C-OT1 = ( 120.889) Reset to = ( 118.750) Dihedral N-CA-C-OT1 = ( -10.768) Distance C-OT2 = ( 1.230) Angle OT1-C-OT2 = ( 122.500) Dihedral CA-OT1-C-OT2 = ( 180.000)==> OT1 NOW : 45.047 28.161 43.976 SUGGESTED : 45.035 28.170 44.021 ==> OT2 NOW : 0.000 0.000 0.000 SUGGESTED : 45.275 26.032 43.872
Check geometry of carboxylate group : Dist C-OT1 = ( 1.230) Dist C-OT2 = ( 1.230) Dist OT1-OT2 = ( 2.157) Angle OT1-C-OT2 = ( 122.500) Angle OT1-C-CA = ( 118.750) Angle OT2-C-CA = ( 118.750) Dih OT1-C-CA-N = ( -10.768) Dih OT2-C-CA-N = ( 169.232) Dih CA-OT1-C-OT2 = (-180.000) ==> YOU MUST ADD/EDIT OT1/OT2 YOURSELF !!!
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (SUGG) alter OLD residue name ? (SOL) HOH NEW residue name ? (HOH) WAT Nr of atoms affected : ( 31) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (LIMI) xplor XPLOR chain label (4 characters) ? ( ) AAAA Residue range to apply (0 0 = all molecule) ? ( 0 138) 1 138 Nr of XPLOR chain labels updated : ( 903) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ_pdb_file) from Chain label*2 to translate ? ( A) Corresponding X-PLOR chain label*4 ? (AAAA) Nr of chain labels translated : ( 3220) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ_pdb_file) xid_ XPLOR chain label*4 to translate ? (AAAA) Corresponding chain label*2 ? ( A) Nr of XPLOR labels translated : ( 1571) Option ? (XID_) XPLOR chain label*4 to translate ? (AAAA) BBBB Corresponding chain label*2 ? ( B) Nr of XPLOR labels translated : ( 1571) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Automagically generate X-PLOR segment IDs and chain IDs;
the first residues will get " A" and "AAAA"; when the
residue-numbering is discontinuous, new IDs are generated
for the next stretch of residues (" B" and "BBBB"), etc.
Breaks in the residue numbering are allowed for water molecules.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ) auto Generating chain and segids ... New chain A, segid AAAA @ residue 1 New chain B, segid BBBB @ residue 39 New chain C, segid CCCC @ residue 78 New chain D, segid DDDD @ residue 93 New chain E, segid EEEE @ residue 106 New chain F, segid FFFF @ residue 120 Nr of segments found : ( 6) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
To split the output PDB file into separate files for X-PLOR, use
something like:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- unix > grep AAAA out.pdb > a.pdb unix > grep BBBB out.pdb > b.pdb ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Or simply use the SPLIt command:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ) auto Generating chain and segids ... New chain A, segid AAAA @ residue 1 New chain B, segid BBBB @ residue 40 New chain C, segid CCCC @ residue 78 ... New chain Q, segid QQQQ @ residue 106 New chain R, segid RRRR @ residue 119 Nr of segments found : ( 18) Option ? (AUTO) splitBasename of PDB files ? (out) h3 New chain id : ( A) New pdb file : (h3a.pdb) Nr of atoms written to it : ( 246) New chain id : ( B) New pdb file : (h3b.pdb) Nr of atoms written to it : ( 236) ... New chain id : ( Q) New pdb file : (h3q.pdb) Nr of atoms written to it : ( 61) New chain id : ( R) New pdb file : (h3r.pdb) Nr of atoms written to it : ( 125) Nr of atoms written in core : ( 2403) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
To change the X-PLOR segment IDs, use something like the
following (or the ASK_ command):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- unix > grep CCCC out.pdb | sed -e s/CCCC/DNA/ > c.pdb unix > grep DDDD out.pdb | sed -e s/DDDD/WATR/ > d.pdb ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This option is similar to the AUTO command, but instead of naming chains and segments A/AAAA, B/BBBB, ..., it asks you to supply the chain and segment names.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (NO_H) ask_ Generating chain and segids ...1 CB ALA 86 3.267 42.575 53.152 1.00 33.06 AAAA New chain name ? ( A) New SEGId name ? (AAAA) New chain A, segid AAAA @ residue 86
2735 C1 NAG 501 7.927 39.505 25.387 1.00 38.20 BBBB New chain name ? ( B) New SEGId name ? (BBBB) New chain B, segid BBBB @ residue 501
2840 CB THR 85 15.420 93.618 100.686 1.00 34.83 KKKK New chain name ? ( C) K New SEGId name ? (KKKK) New chain K, segid KKKK @ residue 85
5581 C1 NAG 501 22.912 85.991 69.990 1.00 24.61 LLLL New chain name ? ( D) L New SEGId name ? (LLLL) New chain L, segid LLLL @ residue 501
5686 O1 HOH 1 2.924 34.893 32.902 1.00 54.85 WWWW New chain name ? ( E) W New SEGId name ? (WWWW) New chain W, segid WWWW @ residue 1
Nr of segments found : ( 5) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ_pdb_file) o2xh Fixing hydrogen names for Asn & Arg Renamed ASN 15 HD2 to HD21 Renamed ASN 15 HD2 to HD22 Renamed ASN 26 HD2 to HD21 Renamed ASN 26 HD2 to HD22 Renamed ARG 30 HH1 to HH11 Renamed ARG 30 HH1 to HH12 Renamed ARG 30 HH2 to HH21 Renamed ARG 30 HH2 to HH22 Renamed ASN 34 HD2 to HD21 ... Renamed ARG 80 HH2 to HH22 Nr of hydrogens renamed : ( 18) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (XPLOr) zone First residue to renumber ? ( 1) 223 Last residue to renumber ? ( 1) 999 NEW number for first residue ? ( 1) 300 Last residue number : ( 331) Nr of atoms changed : ( 58) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (GEOM) resi First NEW residue number ? ( 1) Last residue number : ( 252) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Check if side-chain 1/2 atoms are named correctly. This affects Phe,
Tyr, Asp, Glu and Arg residues. The rule is that the atom which
has the smallest absolute CHI angle should be numbered "1". It
doesn't matter all that much, except when you calculate RMSDs on
all atoms or delta-CHIs for different models/molecules.
This option only lists errors; to correct them, use the option
CORRect_nomenclature.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ_pdb_file) check Nr of atoms : ( 1213) Nr of residues : ( 238)Checking PHE 3 ... ... Checking GLU 137 ...
# of PHE checked : 5 # errors : 0 # of TYR checked : 2 # errors : 0 # of ASP checked : 5 # errors : 0 # of GLU checked : 17 # errors : 0 # of ARG checked : 7 # errors : 0 No problem, mon ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ) check Nr of atoms : ( 3407) Nr of residues : ( 373)Checking GLU 9 ... Checking TYR 17 ... ERROR --- Wrong names for CD1/2 and CE1/2 Torsion CD1 : ( 125.439) Torsion CD2 : ( -52.410)
Checking ASP 29 ... Checking ASP 35 ... Checking TYR 38 ... ERROR --- Wrong names for CD1/2 and CE1/2 Torsion CD1 : ( -97.964) Torsion CD2 : ( 80.065) ... Checking TYR 326 ... ERROR --- Wrong names for CD1/2 and CE1/2 Torsion CD1 : ( 158.234) Torsion CD2 : ( -48.480)
Checking ASP 331 ... Checking GLU 342 ... Checking PHE 359 ... Checking ARG 363 ... Checking ASP 366 ...
# of PHE checked : 8 # errors : 4 # of TYR checked : 19 # errors : 10 # of ASP checked : 21 # errors : 8 # of GLU checked : 10 # errors : 5 # of ARG checked : 6 # errors : 0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Same as CHECk_nomenclature, except that it actually swaps atom names if they are wrong. Note that any attached hydrogen atoms are *NOT* renamed !!!
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (CHECk) corr Nr of atoms : ( 3407) Nr of residues : ( 373)Error in TYR 17 ... Swapped CD1/2 and CE1/2 ... Error in ASP 322 ... Swapped OD1/2
Error in TYR 326 ... Swapped CD1/2 and CE1/2
# of PHE checked : 8 # errors : 4 # of TYR checked : 19 # errors : 10 # of ASP checked : 21 # errors : 8 # of GLU checked : 10 # errors : 5 # of ARG checked : 6 # errors : 0 WARNING - any attached hydrogens NOT renamed ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Use this to apply solutions from rotation function searches to your coordinates.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ_pdb_file) rotate Options: 1 - enter your own rotation matrix 2 - CCP4 (ALMN) Eulerian angles 3 - CCP4 (ALMN) Omega/Phi/Kappa 4 - MERLOT Eulerian angles 5 - MERLOT Polar angles Options 2 - 5 programmed by Rams Option ? ( 1) 3 Omega, Phi, Kappa ? ( 0.000 0.000 0.000) 12 84 182 Nr of atoms rotated : ( 1849) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Use this to apply solutions from translation function searches to your
coordinates.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (ROTAte) trans 1 = Cartesian, 2 = Fractional. Option ? ( 1) 2 Unit cell constants ? ( 100.000 100.000 100.000 90.000 90.000 90.000) 42 42 202 Fractional translation ? ( 0.000 0.000 0.000) 0.13 -0.04 0.52 Nr of atoms translated : ( 1849) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (ROTA) randMax magnitude for shifts (X/Y/Z/B/Q) ? ( 1.000E-01 1.000E-01 1.000E-01 0.000E+00 0.000E+00) 0.03 0.03 0.03 0 0 Maximum shifts : ( 3.000E-02 3.000E-02 3.000E-02 0.000E+00 0.000E+00) Seed for random number generator ? ( 0) 123456 => Random number generator initialised with seed : 123456 Max allowed shifts X/Y/Z/B/Q : ( 3.000E-02 3.000E-02 3.000E-02 0.000E+00 0.000E+00) Average shifts X/Y/Z/B/Q : ( 5.462E-04 -7.776E-04 -4.306E-04 0.000E+00 0.000E+00) RMS shifts X/Y/Z/B/Q : ( 1.729E-02 1.730E-02 1.722E-02 0.000E+00 0.000E+00) AVERAGE POSITIONAL SHIFT : ( 2.870E-02) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Use this for calculating cavity volumes with VOIDOO using several random orientations of your molecule (can also be done inside VOIDOO nowadays)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (RAND) apply Seed for random number generator ? ( 0) 736464 => Random number generator initialised with seed : 736464 Rotations around X,Y,Z (deg) : 153.78 93.32 155.20X Matrix : 1.0000000 0.0000000 0.0000000 0.0000000 -0.8970705 -0.4418874 0.0000000 0.4418874 -0.8970705 Determinant of X rotation matrix : ( 1.000E+00) Y Matrix : -0.0578754 0.0000000 -0.9983238 0.0000000 1.0000000 0.0000000 0.9983238 0.0000000 -0.0578754 Determinant of Y rotation matrix : ( 1.000E+00) Z Matrix : -0.9078057 0.4193911 0.0000000 -0.4193911 -0.9078057 0.0000000 0.0000000 0.0000000 1.0000000 Determinant of Z rotation matrix : ( 1.000E+00) Matrix : 0.0525396 -0.0242724 -0.9983238 0.7766989 0.6293527 0.0255744 0.6276770 -0.7767407 0.0519183 Determinant of random rotation matrix : ( 1.000E+00) Nr of atoms rotated : ( 1849) Option ? (APPLy) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Transform your coordinates from Cartesian to fractional space and vice versa.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Option ? (READ_pdb_file) sequ
1 ME MTL 1 18.690 0.000 8.560 3.12 0.00
2 ME MTL 2 21.410 46.080 2.380 2.87 0.00
Nr of residues found : ( 2)
Option ? (SEQU) frac
Unit-cell constants ? ( 37.130 106.500 40.500 90.000 110.050
90.000)
Matrix : ( 2.693E-02 0.000E+00 0.000E+00)
Matrix : ( 1.177E-09 9.390E-03 0.000E+00)
Matrix : ( 9.829E-03 5.867E-10 2.628E-02)
Nr of atoms converted : ( 2)
Option ? (FRAC) sequ
1 ME MTL 1 0.588 0.000 0.225 3.12 0.00
2 ME MTL 2 0.600 0.433 0.063 2.87 0.00
Nr of residues found : ( 2)
Option ? (SEQU) cart
Unit-cell constants ? ( 37.130 106.500 40.500 90.000 110.050
90.000)
Matrix : ( 3.713E+01 0.000E+00 0.000E+00)
Matrix : ( -4.655E-06 1.065E+02 0.000E+00)
Matrix : ( -1.389E+01 -2.377E-06 3.805E+01)
Nr of atoms converted : ( 2)
Option ? (CART) sequ
1 ME MTL 1 18.690 0.000 8.560 3.12 0.00
2 ME MTL 2 21.410 46.080 2.380 2.87 0.00
Nr of residues found : ( 2)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Invert the coordinates of one or more residues. With this option you can easily produce different stereo-isomers of a compound with a chiral carbon. After the inversion operation, the zone is translated so that it's centre of gravity is at the same position as before. The following example shows how to orthogonalise the fractional coordinates of one enantiomer of a chiral ligand and to generate the symmetry-related one by inversion (spacegroup P1bar):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ_pdb_file)Input PDB file ? (in.pdb) shudo.pdb Number of lines read : ( 27) Number of atoms now : ( 22) Option ? (CRYSt) frac Unit-cell constants ? ( 12.417 9.845 7.864 92.390 99.320 103.430) Matrix : ( 1.242E+01 0.000E+00 0.000E+00) Matrix : ( -2.287E+00 9.576E+00 0.000E+00) Matrix : ( -1.274E+00 -6.413E-01 7.734E+00) Nr of atoms converted : ( 22) Option ? (STAT) writ (...) Option ? (WRIT) invert Residue range to invert (0 0 = all molecule) ? ( 0 0) Nr of atoms affected : ( 22) Translation to apply : ( 16.862 5.835 -2.021) Nr of atoms translated : ( 22) Option ? (STAT) writ (...) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Mirror one or more residues in the YZ, XZ or XY plane. With this option you can easily produce different stereo-isomers of a compound with a chiral carbon. After the mirror operation, the zone is translated so that it's centre of gravity is at the same position as before.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ_pdb_file) stats Nr of atom numbers in memory : ( 903)Item Average St.Dev Min Max ---- ------- ------ --- --- X-coord 0.000 6.833 -18.938 15.666 Y-coord 0.000 9.302 -18.624 23.130 Z-coord 0.000 8.152 -16.378 20.907 B-factor 20.000 0.000 20.000 20.000 Occpncy 1.000 0.000 1.000 1.000
Option ? (STATs) mirr Mirror X, Y, or Z (X/Y/Z) ? (X) Residue range to mirror (0 0 = all molecule) ? ( 0 0) 138 138 Nr of atoms affected : ( 10) Translation to apply : ( 18.368) Nr of atoms translated : ( 10) Option ? (MIRR) stats Nr of atom numbers in memory : ( 903)
Item Average St.Dev Min Max ---- ------- ------ --- --- X-coord 0.000 6.833 -18.938 15.666 Y-coord 0.000 9.302 -18.624 23.130 Z-coord 0.000 8.152 -16.378 20.907 B-factor 20.000 0.000 20.000 20.000 Occpncy 1.000 0.000 1.000 1.000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Translate one or more residues such that their centre-of-gravity ends up at the origin, (0,0,0).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Option ? (READ_pdb_file) stats Nr of atom numbers in memory : ( 903)Item Average St.Dev Min Max ---- ------- ------ --- --- X-coord 65.969 6.833 47.031 81.635 Y-coord 29.006 9.302 10.382 52.136 Z-coord 36.908 8.152 20.530 57.815 B-factor 20.000 0.000 20.000 20.000 Occpncy 1.000 0.000 1.000 1.000
Option ? (STATs) orig Residue range to move (0 0 = all molecule) ? ( 0 0) Nr of atoms affected : ( 903) Translation to apply : ( -65.969 -29.006 -36.908) Nr of atoms translated : ( 903) Option ? (ORIG) stats Nr of atom numbers in memory : ( 903)
Item Average St.Dev Min Max ---- ------- ------ --- --- X-coord 0.000 6.833 -18.938 15.666 Y-coord 0.000 9.302 -18.624 23.130 Z-coord 0.000 8.152 -16.378 20.907 B-factor 20.000 0.000 20.000 20.000 Occpncy 1.000 0.000 1.000 1.000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
None, at present ("peppar, peppar").
Created at Fri Dec 18 19:42:17 1998
by MAN2HTML version 971024/1.6