Program : OOPS
Version : 990311
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 : generation of rebuilding macros for use with O
Package : X-UTIL
Reference(s) for this program:
* 1 * G.J. Kleywegt & T.A. Jones (1994). OOPS-a-daisy. CCP4/ESF-EACBM Newsletter on Protein Crystallography 30, June 1994, pp. 20-24. [http://alpha2.bmc.uu.se/usf/factory_3.html]
* 2 * G.J. Kleywegt & T.A. Jones (1996). Efficient rebuilding of protein structures. Acta Cryst D52, 829-832. [http://www.iucr.ac.uk/journals/acta/tocs/actad/1996/actad5204.html]
* 3 * G.J. Kleywegt & T.A. Jones (1996). Phi/Psi-chology: Ramachandran revisited. Structure 4, 1395-1400. [http://www4.ncbi.nlm.nih.gov/htbin-post/Entrez/query?uid=8994966&form=6&db=m&Dopt=r]
* 4 * G.J. Kleywegt & T.A. Jones (1997). Model-building and refinement practice. Methods in Enzymology 277, 208-230. [http://alpha2.bmc.uu.se/~gerard/gmrp/gmrp.html]
* 5 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
930304 - 0.1 - initial version; analyses pep-flip and rs-fit;
first version of the manual
930305 - 0.2 - include "bad" phi-psi values; read residue
types as well; list diagnostics (optional);
include check for too tight mask
930307 - 0.3 - include checks for too low and too high
temperature factors
930413 - 0.4 - include check on RMS-SIDE-CHAIN (RSC)
930521 - 0.5 - allow one line of O commands in every macro
930610 - 0.6 - create residue property datablock badcounts
930621 - 1.0 - now do RS-fit separately for all atoms, main
chain atoms and side chain atoms; store highest
and lowest temperature factor for each residue
and print them (screen and macro); updated manual;
made executables for ESV and ALPHA
930625 - 1.1 - improve handling of atoms and residues
930626 - 1.2 - deduce PHI/PSI from PDB file rather than reading
it from an O datablock file; added check on
peptide planarity; added check on C-alpha
chirality; print statistics and histograms (where
relevant) before asking for a cut-off value
(optional); revamped manual; print statistics
and histogram of bad-counts
930817 - 1.3 - removed minor bugs; changed 'centre_atom' in
O macros to 'centre_zone' so that it will also
work for non-C-alpha-containing residues
(such as waters)
931101 - 2.0 - allow for user-definable criteria
931102 - 2.1 - exclude PROlines from CA-chirality calculations
since ZETA is ~39-40 degrees rather than ~34
931104 -2.1.1- made default cut-off for peptide planarity
5.8 degrees (instead of 2) in accordance with
the value used by PROCHECK
931108 - 2.2 - include nr of bad contacts (e.g., extracted
from PROCHECK output using ODBM);
produce O2D plot files for certain types
of datablocks;
check consistency of certain datablock names,
types and nr of values in them
940104 -2.2.1- fixed bug: now it also works if your residues
are called "1A", "2A", etc.
940209 - 2.3 - support HETATM cards (treated as in O, i.e.
the residue name gets a "$"-sign in front)
940308 - 3.0 - many more options w.r.t. generated macros;
automatic cut-off for RSfit (if statistics on);
recognise " OT " as main-chain atom; test first
if directory "oops" exists
940413 - 3.1 - hydrogen atoms are now automatically stripped
when a PDB file is read; include checks on
too low and high occupancies; fixed bug in
Ramachandran and peptide-planarity routines
(chain breaks are now recognised); include
QualWat check for waters
940415 - 3.2 - improved O2D plot files
940418 - - cleaned up for the 'real' (paper) manual;
minor bug fix
940810 - 3.3 - added some more plots; some changed Y/N defaults;
more sensible defaults for PDB and MASK file names;
several other minor (cosmetic) changes
940922 - 4.0 - added check on Real-Space R-factor (all atoms);
added check on RMS delta-B bonded atoms (per residue);
added option to create "electronic notebook file";
several minor changes
940923 -4.0.1- fixed some minor bugs w.r.t. user-defined criteria
941204 -4.0.2- fixed silly bugs in RSR-factor and RMS delta-B
bonded bits
941220 - 4.1 - include option to compare current model with a
previous one (e.g., from the previous refinement
cycle)
941223 - 4.2 - include option to create pseudo-PDB file
950211 -4.2.1- include negative RS-fit values; change some Y/N defaults
950311 - 4.3 - fix bug in plot files if > 999 residues; PDB C-terminal
oxygen OTX now recognised as main-chain atom; following
residue types are now recognised as waters: WAT, HOH,
SOL, OHH, HHO, H2O, OH2, H3O, OH3, and (pour nos amis
et amies) EAU; print reminder in last OOPS macro to
clean up the ./oops subdirectory; separate high
temperature-factor cut-off for waters
950330 -4.3.1- minor bug fix (recognize OXT)
950331 - 4.4 - waters no longer included in RS-fit main/side chain
statistics and plots (nor residues with |RS-fit| < 0.0001);
separate RS-fit and RSR cut-offs for waters; in the
comparison with a previous (or related) model, waters
may now be excluded (since they will often have different
names); when comparing to another model, you may now
ask for the values (RMSD etc) to be written to an O
datablock so you can, for instance, colour-ramp your
molecule according to Chi1/Chi2 difference.
950412 -4.4.1- minor bug fix
950912 -4.4.2- tell the user to take a break every time 100 residues have
been checked
951026 - 4.5 - produce a "REMARK 5" file for PDB deposition purposes
960801 -4.5.1- use our new definition of core Ramachandran regions
970204 -4.5.2- no longer use the On_off command in O macros
970625 - 4.6 - option to produce residue-by-residue critique in HTML format
980724 - 4.7 - RS-CC and RS-R cutoffs for waters made identical to those
for other residues; immediate reporting of number and
percentage of outliers for pepflip, RS-CC, RSR and RSC;
in interactive mode, if file opening fails, you get a
new chance
980728 - 4.8 - OOPS now also checks the OMEGA torsion (CA-C-N-CA) when
checking peptide planarity, and will also issue notify
the user of cis-peptides
980914 - 5.0 - OOPS will notify the user of D-amino acids IF the
CA-chirality is checked; if the Ramachandran plot is
checked, unusual PHI torsions can also be listed
(Pro not near -65 degrees; non-Gly > 0); new option
to notify the user of disulfide bridges and to check
for unusual S=S distances and CB-S-S-CB torsions;
increased dimensioning to 7000 residues and 70000 atoms
980929 - 5.1 - since map-contouring has become so fast nowadays, there
is a new option (only available when you use CHAINED
macros) that allows you to go through the residues
starting with the (potentially) worst residue (i.e.,
the one about which OOPS had the highest number of
comments), then the next-worst, etc.
981110 - 5.2 - option to include WHAT IF diagnostics (read from
a file called "pdbout.txt" generated by WHAT IF if the
command "check ful filename.pdb x y" is executed)
990310 - 5.3 - implemented facility that enables you to keep track
of your subjective judgement of every (flagged)
residue; changed default answers to many questions
(mostly from YES to NO); when an OOPS macro is
executed, the current residue name and number will
be shown on the message line
990311 -5.3.1- in case of HETATM residues, the macros will not
be called oops/$300 etc since this confuses O and
makes them more difficult to remove - instead, the
dollar sign will be replaced by an _underscore_;
when reading a PDB file, don't ask for the maximum
CA-CA distance (fixed at 4.5 A)
No more tedious O macros to colour your molecule according to pep-flip and/or rs-fit values etc. OOPS is here to help you !
You provide OOPS with some O datablocks and OOPS will generate O macros which take you from one suspicious residue to the next !
At present OOPS can check:
A - main-chain geometry:
- residues with bad pep-flip values
- residues with PHI-PSI values outside the allowed regions
- Proline residues with PHI not near -65.4 +/- 11.2 degrees
- non-Gly residues with positive PHI
- residues with non-planar peptides
- residues with unusual omega torsion
- residues with a cis-peptide
B - side-chain geometry:
- residues with bad RSC-fit (Rotamer Sidechain) values (version 0.4)
- residues with poor C-alpha chirality
- D-amino acids
C - real-space-fit of model to density:
- RSCC (real-space corr. coeff.) for all atoms
- RSCC for the main chain atoms only
- RSCC for the side chain atoms only
- RS R-factor for all atoms (version 4.0)
D - temperature factors and occupancies:
- residues with at least one atom with a too low B-factor
- ditto, with a too high B-factor
- residues with too high an RMS delta-B for bonded atoms (version 4.0)
- residues with at least one atom with a too low occupancy (version 3.1)
- ditto, with a too high occupancy (version 3.1)
- waters with bad QualWat values (version 3.1)
E - comparison with a previous model:
- positional shifts, changes in temperature factors and occupancies,
large shifts in Phi/Psi and Chi1/Chi2, as well as newly inserted
and mutated residues are flagged since they might warrant your
inspection
F - miscellaneous:
- residues with at least one atom which sticks out of the mask
- residues with bad contacts (version 2.2; requires PROCHECK output)
- residues which violate user-defined criteria (version 2.0)
- disulfide bridges
- disulfides with S=S distance not near 2.06 +/- 0.10 A
- disulfides with CB-S-S-CB not near 96.8 +/- 10.1 degree (right-handed)
or -85.8 +/- 8.6 degrees (left-handed)
- a subset of WHAT IF diagnostics can be extracted from the file
"pdbout.txt" (which is generated if the "check ful file.pdb x y"
command is executed in WHAT IF; version 5.2)
Alternatively, OOPS can be used to generate informative macros for all residues in your protein, and the macros may even have the same name as the residue. So, to centre on residue A273, and to get a message about what is suspicious about this residue, all you need to type is: @oops/a273
Before you run OOPS, create a directory called "oops" in your current O directory. OOPS will write most of the macros to that directory so these files won't clutter your working O directory (use: "mkdir oops" to create this directory).
NOTE: OOPS WILL NOT WORK IF YOU DON'T HAVE A SUBDIRECTORY CALLED oops !!!
Also, you will need AT LEAST a file containing the residue names as an O datablock and another which contains the residue types as a datablock. In addition, you may need the pep-flip, rs-fit and rsc datablocks of your current molecule, a PDB file of your current model and a mask file (in any MAMA format; see the MAMA manual).
If your current molecule is called RIGA, for example, then type: "dir riga*" in O to get a list of datablocks. Then write the appropriate datablocks to files, e.g.:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- write riga_residue_name resnam.o ; write riga_residue_type restyp.o ; write riga_residue_pepflip pepflip.o ; write riga_residue_rsfit rsfit_all.o ; ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
There is a macro called "pre_oops.omac" in the OMAC directory which will calculate RS-fit (all atoms, main-chain and side-chain), pep-flip and rsc values for your current model and create the datablock files needed by OOPS. Check it out !
Now you are ready to run OOPS. Just run the program and answer the following questions:
- analyse too high temperature factors ? if so, and the PDB file hasn't been read yet, supply the name of the PDB file; also supply a cut-off. If you already analysed too low temperature factors, you will not get statistics again
- analyse too high RMS delta-B bonded atoms ? if so, and the PDB file hasn't been read yet, supply the name of the PDB file; also supply a distance cut-off. The values are calculated for each residue separately; bonds to atoms in sequentially neighbouring residues are included as well (e.g. N-C).
- analyse too high occupancies ? if so, and the PDB file hasn't been read yet, supply the name of the PDB file; also supply a cut-off. If you already analysed too low occupancies, you will not get statistics again
- do you want CHAINED macros ? If so, each macro will "point to" the next one; it will put an O instruction on the O menu to execute the next macro. If you want to be use OOPS as an information-macro-generator, select NO; for rebuilding of only suspicious residues, select YES
- do you want macros to have the same name as the residue to which they relate ? If so, the macro for residue B107 will be called oops/b107 (note: lowercase); if not, the macros will be called oops/1, oops/2 etc.
OOPS will then loop over all residues. If a residue has a bad pep-flip or rs-fit value etc., a macro will be written to the oops subdirectory (unless you requested macros for ALL residues). In addition, a start-up macro called "oops.mac" will be put in your current directory.
In the case of pepflip values etc., only residues which have absolute values greater than 0.01 are considered (this is to prevent OOPS from flagging all your waters as having bad RS-fit values, or your terminal residues as having bad PHI/PSI values). Similar safe-guards are applied for other attributes (e.g.: RS-fit side-chain not for GLYs; RSC not for GLY/ALA; phi/psi not for N- and C-terminal residues, etc. etc.).
When OOPS is finished (and if there were any bad residues), all you have to do is type: "@oops.omac" from within O. This will then automatically centre on the first bad residue and print a message which tells you what is suspicious about this residue. In addition, a new menu item "@oops/2" will be added to your menu. When you're finished with the first residue, just click on this new menu item to go the second suspicious residue automatically, etc. ad infinitum. When the second macro is executed, you again will be centred on this residue's C-alpha atom, a diagnostic message is printed, the previous menu item "@oops/2" is deleted and a new one, "@oops/3" is inserted. Again, when you're finished, just click on "@oops/3" and voila.
After the last "baddy", the terminal bell will ring and a message that there aren't any more of them is printed.
From version 5.3 on, a facility has been implemented that enables you to keep track of your subjective judgement of all the residues you inspect with the OOPS macros.
As you execute the "oops.omac" start-up macro, four new commands
will be added to your menu:
- @Good_fit
- @Poor_fit
- @Poor_dens
- @No_dens
Also, a new datablock will be created (and filled with zeros)
that is called MOLNAM_residue_quality (MOLNAM is the name
of the molecule you are scrutinising, e.g. M9). Now, whenever
you inspect a residue, you can click on any of the four new
commands, and the entry of the current residue will be set
to:
- 0 if you click on @Good_fit: the density is good, and the fit
of the model to the density is good
- 1 if you click on @Poor_fit: the density is good, but the fit
of the model to the map is not, i.e. you need to do some
rebuilding
- 2 if you click on @Poor_dens: the density is poor, so you cannot
fit the residue any better than it is
- 3 if you click on @No_dens: there is no density, so you cannot
reasonably fit the residue at all
While you are still working on the same residue, you can revise
your judgement, and press another of the four commands.
When you are done, a new CA-object will be generated (called QUAL), where residues with quality value 0 are blue, value 1 red (these should have been fixed by you), value 2 magenta (may have been rebuilt in the hopes of better density next cycle), and value 3 white (no density, little hope at present). You can use this object, for example, to ask a colleague or your supervisor to have a (quick) look at the problematic residues.
You can also use it in a next rebuilding cycle to quickly skip over residues that are flagged as outliers (e.g., in pepflip or rotamer analysis), but for which you know that the density and the fit to it are rock solid.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- O > rsr_map m5_4.map rs_fit m6a a5 a162 ... O > wr m6a_residue_rsfit rsfit_all.o ; O > read odat/rsfit_mc.o rs_fit m6a a5 a162 ... O > wr m6a_residue_rsfit rsfit_mc.o ; O > read odat/rsfit_sc.o O > rs_fit m6a a5 a162 ... O > wr m6a_residue_rsfit rsfit_sc.o ; O > pep_flip m6a a5 a162 ... O > wr M6A_RESIDUE_PEPFLIP pepflip.o ; O > rsc m6a a5 a162 O > wr m6a_residue_rsc rsc.o ; O > wr M6A_RESIDUE_NAME resnam.o ; O > wr M6A_RESIDUE_TYPE restyp.o ; O > s_a_o m6a.pdb m6a ;;;;; Sam> Coordinate file type assumed from file name is PDB Sam> 1280 atoms written out. ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 181 gerard rigel 20:04:34 o/m5_6 > run oops ... Max nr of residues : 5000 Max size of mask : 4194304 Max nr of atoms : 50000 Max nr of user-defined criteria : 10Print statistics and histograms ? (Y) y Auto-generate (some) O2D plot files ? (Y) y
Molecule name in O ? (M1) m6a
O data block with residue names ? (resnam.o) Datablock : (M6A_RESIDUE_NAME) Data type : (C) Number : (158) Format : ((1x,5a))
O data block with residue types ? (restyp.o) Datablock : (M6A_RESIDUE_TYPE) Data type : (C) Number : (158) Format : ((1x,5a)) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
For every criterion you want to check, you will have to provide one or more filenames and one or more cut-off values etc. E.g.:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Analyse pep-flip values ? (Y) O data block with pep-flip values ? (pepflip.o) Datablock : (M6A_RESIDUE_PEPFLIP) Data type : (R) Number : (158) Format : ((8f8.3))*************************************************************************** Analysis of Pep-flip values (>0) ***************************************************************************
Number of values .................... 154 Average value ....................... 0.837 Standard deviation .................. 0.584 Minimum value observed .............. 0.166 Maximum value observed .............. 3.033
Nr < 0.0000 : 0 ( 0.00 %; Cum 0.00 %) Nr >= 0.0000 and < 0.2500 : 6 ( 3.90 %; Cum 3.90 %) Nr >= 0.2500 and < 0.5000 : 41 ( 26.62 %; Cum 30.52 %) Nr >= 0.5000 and < 0.7500 : 45 ( 29.22 %; Cum 59.74 %) Nr >= 0.7500 and < 1.0000 : 29 ( 18.83 %; Cum 78.57 %) Nr >= 1.0000 and < 1.2500 : 5 ( 3.25 %; Cum 81.82 %) Nr >= 1.2500 and < 1.5000 : 9 ( 5.84 %; Cum 87.66 %) Nr >= 1.5000 and < 1.7500 : 2 ( 1.30 %; Cum 88.96 %) Nr >= 1.7500 and < 2.0000 : 6 ( 3.90 %; Cum 92.86 %) Nr >= 2.0000 and < 2.2500 : 6 ( 3.90 %; Cum 96.75 %) Nr >= 2.2500 and < 2.5000 : 1 ( 0.65 %; Cum 97.40 %) Nr >= 2.5000 and < 2.7500 : 1 ( 0.65 %; Cum 98.05 %) Nr >= 2.7500 and < 3.0000 : 2 ( 1.30 %; Cum 99.35 %) Nr >= 3.0000 and < 3.2500 : 1 ( 0.65 %; Cum 100.00 %) Nr >= 4.7500 : 0 ( 0.00 %; Cum 100.00 %)
O2D plot file ? (m6a_pepflip.plt) Plot file written
Pep-flip cut-off ? ( 2.500) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Compare with previous model ? (Y)PDB file of previous model ? (m18_prev.pdb) m16.pdb REMARK ( Created by MOLEMAN V. 940525/4.9.1 at Mon Jul 25 20:22:45 1994 for user) REMARK ( model M16 xplor crabp II 940725) ... SCALE3 ( 0.000000 0.000000 0.012885 0.00000) Not in current model : O1 HOH 331 Not in current model : O1 HOH 403 Not in current model : O1 HOH 404 Not in current model : O1 HOH 408 Not in current model : O1 HOH 411 ... Not in current model : O1 HOH 542 END ( ) Nr of atoms read : ( 1215) Nr of atoms found : ( 1200)
Inserted residue > HOH 600 Inserted residue > HOH 601 Inserted residue > HOH 602 Inserted residue > HOH 603 ... Inserted residue > HOH 612
Name of this previous model ? (Prev Model)
Comparing with previous model
*************************************************************************** Analysis of RMSD current/previous model ***************************************************************************
Number of values .................... 238 Average value ....................... 0.391 Standard deviation .................. 0.813 Minimum value observed .............. 0.000 Maximum value observed .............. 5.671
Nr < 0.0000 : 0 ( 0.00 %; Cum 0.00 %) Nr >= 0.0000 and < 0.1000 : 115 ( 48.32 %; Cum 48.32 %) Nr >= 0.1000 and < 0.2000 : 49 ( 20.59 %; Cum 68.91 %) Nr >= 0.2000 and < 0.3000 : 23 ( 9.66 %; Cum 78.57 %) Nr >= 0.3000 and < 0.4000 : 10 ( 4.20 %; Cum 82.77 %) ... *************************************************************************** Analysis of Phi/Psi distance ***************************************************************************
Number of values .................... 238 Average value ....................... 1.228 Standard deviation .................. 1.632 Minimum value observed .............. 0.000 Maximum value observed .............. 12.650
Nr < 0.0000 : 0 ( 0.00 %; Cum 0.00 %) Nr >= 0.0000 and < 10.0000 : 237 ( 99.58 %; Cum 99.58 %) Nr >= 10.0000 and < 20.0000 : 1 ( 0.42 %; Cum 100.00 %) Nr >= 180.0000 : 0 ( 0.00 %; Cum 100.00 %)
O2D plot file ? (m18_phipsi.plt) Plot file written
*************************************************************************** Analysis of Chi1/2 distance ***************************************************************************
Number of values .................... 238 Average value ....................... 4.160 Standard deviation .................. 13.168 Minimum value observed .............. 0.000 Maximum value observed .............. 137.104
Nr < 0.0000 : 0 ( 0.00 %; Cum 0.00 %) Nr >= 0.0000 and < 10.0000 : 219 ( 92.02 %; Cum 92.02 %) Nr >= 10.0000 and < 20.0000 : 9 ( 3.78 %; Cum 95.80 %) Nr >= 20.0000 and < 30.0000 : 2 ( 0.84 %; Cum 96.64 %) Nr >= 40.0000 and < 50.0000 : 3 ( 1.26 %; Cum 97.90 %) Nr >= 50.0000 and < 60.0000 : 3 ( 1.26 %; Cum 99.16 %) Nr >= 80.0000 and < 90.0000 : 1 ( 0.42 %; Cum 99.58 %) Nr >= 130.0000 and < 140.0000 : 1 ( 0.42 %; Cum 100.00 %) Nr >= 180.0000 : 0 ( 0.00 %; Cum 100.00 %)
O2D plot file ? (m18_chi12.plt) Plot file written
Maximum RMSD (A) ? ( 0.500) Maximum RMS delta-B (A2) ? ( 5.000) Maximum RMS delta-Q (A2) ? ( 0.100) Maximum Phi/Psi distance ? ( 20.000) Maximum Chi1/2 distance ? ( 20.000) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
From version 5.2 on, OOPS can read "pdbout.txt" files created by WHAT IF (command: "check ful filename.pdb x y"). A subset of the diagnostics is used literally by OOPS.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Include WHAT IF diagnostics ? (N) y WHAT IF report file ? (pdbout.txt) Ouch : (# 1 # Warning: Rounded coordinates detected) Rounded coordinates : ( 5) Ouch : (# 3 # Warning: Valine nomenclature problem) Incorrect Valine nomenclature : ( 1) Ouch : (# 4 # Error: Threonine nomenclature problem) Incorrect Threonine nomenclature : ( 1) No incorrect Isoleucine nomenclature Ouch : (# 6 # Warning: Leucine nomenclature problem) Incorrect Leucine nomenclature : ( 1) Ouch : (# 7 # Warning: Arginine nomenclature problem) Incorrect Arginine nomenclature : ( 1) Ouch : (# 13 # Warning: Chirality deviations detected) Chirality deviation : ( 7) Ouch : (# 16 # Error: Weights outside the 0.0 -- 1.0 range) Impossible occupancy : ( 1) Ouch : (# 17 # Warning: Missing atoms) Missing atoms : ( 4) Ouch : (# 20 # Warning: Unusual bond lengths) Unusual bond lengths : ( 18) Ouch : (# 23 # Warning: Unusual bond angles) Unusual bond angles : ( 35) Ouch : (# 25 # Error: Side chain planarity problems) Non-planar side chains : ( 1) Ouch : (# 26 # Error: Connections to aromatic rings out of plane) Atoms not co-planar with rings : ( 1) Ouch : (# 29 # Warning: Torsion angle evaluation shows unusual residues) Unusual torsion angles : ( 2) Ouch : (# 30 # Warning: Backbone torsion angle evaluation shows unusual conformations) Unusual backbone torsions : ( 6) Ouch : (# 38 # Error: Atoms too close to symmetry axes) Atoms near symmetry axes : ( 2) Ouch : (# 39 # Error: Abnormally short interatomic distances) ERROR --- While trying to recognise residue > ( 13 LYS ( 13 ) A NZ -- 130 LEU ( OXT ) A O2 0.161 2.539 INTRA) Short contacts : ( 76) Ouch : (# 40 # Warning: Abnormal packing environment for some residues) Abnormal packing environments : ( 7) Ouch : (# 48 # Warning: Backbone oxygen evaluation) Unusual peptide oxygens : ( 1) No unusual rotamers Ouch : (# 50 # Warning: Unusual backbone conformations) Unusual backbone conformations : ( 9) Ouch : (# 52 # Error: Water clusters without contacts with non-water atoms) Isolated water clusters : ( 5) Ouch : (# 53 # Warning: Water molecules need moving) Waters in wrong asymmetric unit : ( 9) Ouch : (# 54 # Error: Water molecules without hydrogen bonds) Water molecules without H-bonds : ( 5) Ouch : (# 59 # Error: HIS, ASN, GLN side chain flips) H/N/Q side chain flips : ( 2) Ouch : (# 61 # Warning: Buried unsatisfied hydrogen bond donors) Unsatisfied H-bond donors : ( 5) No unsatisfied H-bond acceptors Nr of WHAT IF diagnostics : ( 205) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- User-definable criteria Max number of them : ( 10)Enter file with user datablock (<CR> to stop): ( ) rsrfree_zone.o Datablock : (M18_RESIDUE_RSRFREE) Data type : (R) Number : (238) Format : ((f10.3)) Name of the property ? (User-criterion nr 1) RSRfree Warning for bad residues in O ? (Bad RSRfree; value =)
*************************************************************************** Analysis of RSRfree ***************************************************************************
Number of values .................... 238 Average value ....................... 0.292 Standard deviation .................. 0.090 Minimum value observed .............. 0.182 Maximum value observed .............. 0.554
Nr < 0.1448 : 0 ( 0.00 %; Cum 0.00 %) Nr >= 0.1820 and < 0.2192 : 52 ( 21.85 %; Cum 21.85 %) Nr >= 0.2192 and < 0.2564 : 65 ( 27.31 %; Cum 49.16 %) Nr >= 0.2564 and < 0.2936 : 34 ( 14.29 %; Cum 63.45 %) Nr >= 0.2936 and < 0.3308 : 16 ( 6.72 %; Cum 70.17 %) Nr >= 0.3308 and < 0.3680 : 27 ( 11.34 %; Cum 81.51 %) Nr >= 0.3680 and < 0.4052 : 11 ( 4.62 %; Cum 86.13 %) Nr >= 0.4052 and < 0.4424 : 12 ( 5.04 %; Cum 91.18 %) Nr >= 0.4424 and < 0.4796 : 10 ( 4.20 %; Cum 95.38 %) Nr >= 0.4796 and < 0.5168 : 4 ( 1.68 %; Cum 97.06 %) Nr >= 0.5168 and < 0.5540 : 6 ( 2.52 %; Cum 99.58 %) Nr >= 0.5540 : 1 ( 0.42 %; Cum 100.00 %)
A residue has a BAD "RSRfree" IF: its value either > CUTOFF or < CUTOFF Should I use ">" or "<" ? (>) > Cut-off value to use ? ( 4.710E-01) 0.45 Checking ...
Enter file with user datablock (<CR> to stop): ( )
Nr of user criteria : ( 1) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
After all input has been given, tell OOPS what output you want:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- You may opt to get the details listed on the screen. Do you want to see the details ? (Y)Also, you can get this list written to a file; this is very handy for electronic note-keeping: just edit the file as you rebuild your model & print it & stick it in your notebook ! Do you want to have a list file ? (Y) Name of the list file ? (m18_rebuild.notes)
You may enter one line of O commands which will be executed by EVERY macro generated by OOPS. O command(s) to execute in every macro ? (bell print DONE) @fast_dials
You may opt to get chained macros for ALL or merely the BAD residues. Do you want macros for ALL residues ? (N)
You may opt to get chained macros or individual macros without instructions to put the next macro on the menu. Do you want CHAINED macros ? (Y)
You may opt to give the macros the same name as the residue which they deal with (in lowercase), or to just give them sequential numbers (1, 2, ...). Do you want macros named as RESIDUES ? (Y)
OOPS - (PRO 2) Large positional shift; RMSD = 0.68 Large Chi1/2 shift; RMSD = 26.76 OOPS - (LYS 9) Bad RSC = 2.29 OOPS - (ASN 15) Bad RSC = 1.76 Bad Phi-Psi = 65.46 22.91 OOPS - (GLU 17) Large positional shift; RMSD = 1.04 ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
At the end, an overview is printed:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... OOPS - (HOH 612) Bad RS-fit (all atoms) = 0.539 Newly inserted residue in this modelNr of baddies : ( 83)
Start by typing @oops.omac in O !!!
Bad pep-flip : ( 2) Bad RS-fit (all atoms) : ( 16) Bad RS-fit (main chain) : ( 0) Bad RS-fit (side chain) : ( 0) Bad RS R-factor (all atoms) : ( 16) Bad RSC : ( 12) Bad mask : ( 0) Bad B (low) : ( 0) Bad B (high) : ( 26) Bad RMS delta-B bonded atoms : ( 1) Bad Q (low) : ( 0) Bad Q (high) : ( 0) Bad Phi/Psi : ( 3) Bad peptide planarity : ( 0) Bad C-alpha chirality : ( 1) Newly inserted residues : ( 13) Newly mutated residues : ( 0) Large positional shift : ( 57) Large temp.-factor shift : ( 0) Large occupancy shift : ( 0) Large Phi/Psi shift : ( 0) Large Chi1/2 shift : ( 10) Bad QualWat : ( 0) Bad contact(s) : ( 0) Bad RSRfree : ( 19)
Read oops_badcounts.o into O and use residue property badcounts to colour your molecule, or plot this file, to reveal areas where the structure is poor.
*************************************************************************** Analysis of Bad counts ***************************************************************************
Number of values .................... 238 Average value ....................... 0.647 Standard deviation .................. 1.178 Minimum value observed .............. 0.000 Maximum value observed .............. 6.000
Nr < 0.0000 : 0 ( 0.00 %; Cum 0.00 %) Nr >= 0.0000 and < 1.0000 : 163 ( 68.49 %; Cum 68.49 %) Nr >= 1.0000 and < 2.0000 : 31 ( 13.03 %; Cum 81.51 %) Nr >= 2.0000 and < 3.0000 : 23 ( 9.66 %; Cum 91.18 %) Nr >= 3.0000 and < 4.0000 : 14 ( 5.88 %; Cum 97.06 %) Nr >= 4.0000 and < 5.0000 : 3 ( 1.26 %; Cum 98.32 %) Nr >= 5.0000 and < 6.0000 : 1 ( 0.42 %; Cum 98.74 %) Nr >= 6.0000 and < 7.0000 : 3 ( 1.26 %; Cum 100.00 %) Nr >= 24.0000 : 0 ( 0.00 %; Cum 100.00 %)
O2D plot file ? (m18_badcounts.plt) Plot file written
*** OOPS *** OOPS *** OOPS *** OOPS *** OOPS *** OOPS *** OOPS *** OOPS ***
Version - 941220/4.1 Started - Tue Dec 20 22:52:26 1994 Stopped - Tue Dec 20 23:00:33 1994
CPU-time taken : User - 5.8 Sys - 3.3 Total - 9.1
*** OOPS *** OOPS *** OOPS *** OOPS *** OOPS *** OOPS *** OOPS *** OOPS ***
>>> This program (C) 1993-94, GJ Kleywegt & TA Jones <<< E-mail: "gerard@xray.bmc.uu.se" or "alwyn@xray.bmc.uu.se"
*** OOPS *** OOPS *** OOPS *** OOPS *** OOPS *** OOPS *** OOPS *** OOPS ***
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- print Created by OOPS V. 941220/4.1 at Tue Dec 20 23:00:21 1994 for user gerard print Molecule M18 print OOPS has checked: print Pep-flip values; cutoff = 2.500000 print RS-fit (all atoms); cutoff = 0.7000000 print RS R-factor (all atoms); cutoff = 0.4000000 print RSC values; cutoff = 1.500000 print Too high temperature factors; cutoff = 40.00000 print Too high RMS delta-B bonded atoms; cutoff = 5.000000 print Phi-Psi angle combinations (Ramachandran) print Peptide planarity; cutoff = 5.800000 print CA chirality; cutoff = 3.500000 print Comparison with previous model Prev Model print RMSD; cutoff = 0.5000000 print RMS delta-B; cutoff = 5.000000 print RMS delta-Q; cutoff = 0.1000000 print Phi/Psi distance; cutoff = 20.00000 print Chi1/2 distance; cutoff = 20.00000 print RSRfree cut-off = 0.4500000 print Macros were generated for BAD residues print Macros were chained together print Macros were given residue names mol M18 @oops/2 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
an actual residue macro may look like this:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 1493 gerard rigel 18:55:56 oops/exam > cat oops/104 centre_zone M18 104 ; print Residue GLU 104 print Bad RS-fit (all atoms) = 0.662 print Bad RSC = 1.80 print Too high temperature factor = 53.12 print Large positional shift; RMSD = 1.14 print Large Chi1/2 shift; RMSD = 48.77 print Bad RSRfree; value = 0.4530000 @fast_dials print Hit or type "@oops/107" for next baddy menu @oops/107 on on_off menu @oops/104 off on_off ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ... O > @oops.omac O > Macro in computer file-system. As4> Created by OOPS V. 931108/2.2 at Mon Nov 8 22:28:52 1993 for user O > As4> Molecule M8A O > As4> OOPS has checked: O > As4> Pep-flip values; cutoff = 2.500000 O > As4> RS-fit (all atoms); cutoff = 0.5500000 O > As4> RSC values; cutoff = 1.500000 O > As4> Phi-Psi angle combinations O > As4> Peptide planarity; cutoff = 5.800000 O > As4> CA chirality; cutoff = 3.500000 O > As4> Number of bad contacts; cutoff = 1 O > O > O > Macro in computer file-system. As4> No object defined. As4> M8A A1 A1 M8A As4> Centering on zone from A1 to A1 O > As4> Residue PRO A1 O > As4> Bad contact(s); count = 1 O > As4> Bad XPLOR GeomPlot; value = 4.706100 O > As4> Hit or type "@oops/2" for next baddy O > O > O > O > Macro in computer file-system. ... As4> M8A A2 A2 SPH As4> Centering on zone from A2 to A2 O > As4> Residue SER A2 O > As4> Bad Phi-Psi = 109.16 155.57 O > As4> Non-planar peptide; improper = -8.08 O > As4> Bad CA chirality; zeta = 28.24 O > As4> Bad XPLOR GeomPlot; value = 9.952900 O > As4> Hit or type "@oops/3" for next baddy O > O > O > O > Macro in computer file-system. ... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Created by OOPS V. 941220/4.1 at Tue Dec 20 23:00:21 1994 for user gerard Molecule M18 OOPS has checked: Pep-flip values; cutoff = 2.500000 RS-fit (all atoms); cutoff = 0.7000000 RS R-factor (all atoms); cutoff = 0.4000000 RSC values; cutoff = 1.500000 Too high temperature factors; cutoff = 40.00000 Too high RMS delta-B bonded atoms; cutoff = 5.000000 Phi-Psi angle combinations (Ramachandran) Peptide planarity; cutoff = 5.800000 CA chirality; cutoff = 3.500000 Comparison with previous model Prev Model RMSD; cutoff = 0.5000000 RMS delta-B; cutoff = 5.000000 RMS delta-Q; cutoff = 0.1000000 Phi/Psi distance; cutoff = 20.00000 Chi1/2 distance; cutoff = 20.00000 RSRfree cut-off = 0.4500000OOPS - PRO - 2 Large positional shift; RMSD = 0.68 Large Chi1/2 shift; RMSD = 26.76
OOPS - LYS - 9 Bad RSC = 2.29
OOPS - ASN - 15 Bad RSC = 1.76 Bad Phi-Psi = 65.46 22.91
OOPS - GLU - 17 Large positional shift; RMSD = 1.04
OOPS - GLU - 18 Bad RSC = 2.31
OOPS - LYS - 21 Large positional shift; RMSD = 1.06 Large Chi1/2 shift; RMSD = 45.87
...
OOPS - HOH - 611 Newly inserted residue in this model
OOPS - HOH - 612 Bad RS-fit (all atoms) = 0.539 Newly inserted residue in this model
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
From version 4.5 onward, OOPS automatically produces a file called oops_remarks.pdb. This file contains statistics for some of the checks that OOPS has performed (provided you said you wanted statistics listed). You can include this file in your PDB deposition form.
The file may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- REMARK 5 REMARK 5 CREATED BY : OOPS REMARK 5 VERSION : 951026/4.5 REMARK 5 MODEL NAME : M9 REMARK 5 DATE : THU MAR 2 01:45:04 1995 REMARK 5 REMARK 5 MODEL QUALITY REMARK 5 REMARK 5 PEPTIDE-OXYGEN ORIENTATION REMARK 5 PROGRAM USED: O REMARK 5 NR OF RESIDUES : 718 REMARK 5 MAXIMUM VALUE (A) : 3.51 REMARK 5 AVERAGE VALUE (A) : 0.77 REMARK 5 CUT-OFF VALUE (A) : 2.50 REMARK 5 OUTLIERS (NR) : 22 REMARK 5 OUTLIERS (%) : 3.06 REMARK 5 REMARK 5 ROTAMER SIDECHAIN ANALYSIS REMARK 5 PROGRAM USED: O REMARK 5 NR OF RESIDUES : 568 REMARK 5 MAXIMUM VALUE (A) : 2.82 REMARK 5 AVERAGE VALUE (A) : 0.59 REMARK 5 CUT-OFF VALUE (A) : 1.50 REMARK 5 OUTLIERS (NR) : 36 REMARK 5 OUTLIERS (%) : 6.34 REMARK 5 REMARK 5 REAL-SPACE FIT (CORR. COEFF./ALL ATOMS) REMARK 5 PROGRAM USED: O REMARK 5 NR OF RESIDUES : 1250 REMARK 5 MINIMUM VALUE : 0.18 REMARK 5 AVERAGE VALUE : 0.88 REMARK 5 STANDARD DEVIATION : 0.11 REMARK 5 CUT-OFF VALUE : 0.60 REMARK 5 OUTLIERS (NR) : 30 REMARK 5 OUTLIERS (%) : 2.40 REMARK 5 REMARK 5 REAL-SPACE FIT (CORR. COEFF./MAINCHAIN) REMARK 5 PROGRAM USED: O REMARK 5 NR OF RESIDUES : 744 REMARK 5 MINIMUM VALUE : 0.51 REMARK 5 AVERAGE VALUE : 0.92 REMARK 5 STANDARD DEVIATION : 0.05 REMARK 5 CUT-OFF VALUE : 0.80 REMARK 5 OUTLIERS (NR) : 32 REMARK 5 OUTLIERS (%) : 4.30 REMARK 5 REMARK 5 REAL-SPACE FIT (CORR. COEFF./SIDECHAIN) REMARK 5 PROGRAM USED: O REMARK 5 NR OF RESIDUES : 684 REMARK 5 MINIMUM VALUE : 0.51 REMARK 5 AVERAGE VALUE : 0.92 REMARK 5 STANDARD DEVIATION : 0.05 REMARK 5 CUT-OFF VALUE : 0.70 REMARK 5 OUTLIERS (NR) : 10 REMARK 5 OUTLIERS (%) : 1.46 REMARK 5 REMARK 5 PEPTIDE PLANARITY IMPROPER TORSION REMARK 5 PROGRAM USED: OOPS REMARK 5 NR OF RESIDUES : 724 REMARK 5 MINIMUM VALUE (DEG) : -3.18 REMARK 5 MAXIMUM VALUE (DEG) : 4.70 REMARK 5 AVERAGE VALUE (DEG) : 0.09 REMARK 5 STANDARD DEVIATION (DEG) : 1.02 REMARK 5 CUT-OFF VALUE (DEG) : 5.80 REMARK 5 OUTLIERS (NR) : 0 REMARK 5 OUTLIERS (%) : 0.00 REMARK 5 REMARK 5 CA CHIRALITY IMPROPER TORSION REMARK 5 PROGRAM USED: OOPS REMARK 5 NR OF RESIDUES : 620 REMARK 5 MINIMUM VALUE (DEG) : 29.43 REMARK 5 MAXIMUM VALUE (DEG) : 37.48 REMARK 5 AVERAGE VALUE (DEG) : 34.12 REMARK 5 STANDARD DEVIATION (DEG) : 1.08 REMARK 5 CUT-OFF VALUE (DEG) : 3.50 REMARK 5 OUTLIERS (NR) : 4 REMARK 5 OUTLIERS (%) : 0.65 REMARK 5 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
colouring your molecule according to the number of violations:
EXAMPLE 1:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- O > read oops_badcounts.o O > mol m6a O > pai_ramp residue_badcounts ; blue red O > obj bad ca ; end ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
EXAMPLE 2:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- O > read oops_badcounts.o O > mol m6a O > pai_prop atom_name = ca blue O > pai_prop residue_badcounts > 0 red O > obj bad ca ; end ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
EXAMPLE 3:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- O > read oops_badcounts.o O > mol m6a O > pai_case residue_badcounts 5 0 1 2 3 4 blue green yellow orange red O > obj bad ca ; end ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
use ODBM or ODBMAN to create O-style datablock files from ASCII files.
Example: run the "geomplot" XPLOR script for your molecule(s),
then extract the residue values with ODBMAN from the file
called geomplot.list.
ODBMAN and ODBM can also be used to extract several types of
datablock from a PROCHECK output file (see their manuals) !
when prompted by OOPS to supply a line of O commands which
will be executed for every bad residue, be clever and execute
a macro ! For example: @do_all.omac
You may then change the contents of this macro later on without
having to re-run OOPS.
Use the OMAC/pre_oops.omac macro to take some work out of your hands (this enables you to have a coffee or a beer while O crunches).
Converting the O2D plot files generated by OOPS into PostScript format is conveniently done with the OMAC/o2dps script, for instance:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 189 gerard rigel 20:04:34 o/m5_6 > o2dps '*.plt' 1d... o2dps ... convert O2D plot files to PostScript ...
Will convert m6a_badcounts.plt to m6a_badcounts.ps with option 1d ... Will convert m6a_pepflip.plt to m6a_pepflip.ps with option 1d ... Will convert m6a_rsc.plt to m6a_rsc.ps with option 1d ... Will convert m6a_rsfit_all.plt to m6a_rsfit_all.ps with option 1d ... Will convert m6a_rsfit_mc.plt to m6a_rsfit_mc.ps with option 1d ... Will convert m6a_rsfit_sc.plt to m6a_rsfit_sc.ps with option 1d ...
Running O2D ...
Lowest X-value : ( 0.000E+00) ... Highest Y-value : ( 1.000E+00) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
OOPS always checks if the names of datablocks are consistent, to help you prevent using a datablock belonging to an old model:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Analyse RS R-factor (all atoms) ? (Y) O data block with RS R-factors ? (rsrfac_all.o) Datablock : (M18_RESIDUE_RSRCONV) Data type : (R) Number : (238) Format : ((f10.3)) WARNING - inconsistent datablock name Expected : (m18_residue_rsfit) Encountered : (m18_residue_rsrconv) Continue anyway ? (Y) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If you want to have a pseudo-PDB file, you can do this as follows in OOPS:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- You can also get a "pseudo-PDB file" with one CA atom for each residue which has: X = Phi(residue) Y = Psi Z = Pep-flip * 100 B = Maximum temp. factor Q = RSC Displaying and colouring this "molecule" in O may reveal poor areas and correlations between poor Phi/Psi and Pep-flip values Create pseudo-PDB file ? (Y) Name of the PDB file ? (m18_pseudo.pdb) Name of the O datablock file ? (m18_pseudo.odb) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
In O, do something like this:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- O > s_a_i m18_pseudo.pdb pse O > mol pse O > pa_prop Paint> Property? [atom_name]: atom_wt Paint> Operator (< > <= >= ^= [=]): > Paint> Value? []: 1.5 Paint> Colour? [red]: O > pa_prop Paint> Property? [atom_name]: atom_b Paint> Operator (< > <= >= ^= [=]): > Paint> Value? []: 40 Paint> Colour? [red]: O > zone ; end O > read m18_pseudo.odb Heap> Heap> Type: draw ramaflip Heap> O > draw ramaflip O > ske_cpk pse ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
You can now click on Ramachandran plot outliers etc.
None, at present.
Created at Thu Mar 11 21:57:30 1999
by MAN2HTML version 971024/1.6