Program : ODBMAN
Version : 990303
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 : manipulate O datablocks
Package : X-UTIL
Reference(s) for this program:
* 1 * G.J. Kleywegt (1997). Les amis d"O. CCP4/ESF-EACBM Newsletter on Protein Crystallography 34, September 1997, pp. 5-8. [http://alpha2.bmc.uu.se/usf/factory_8.html]
* 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.
931115 - 0.1 - initial version
931129 - 0.4 - first production version
931130 - 0.5 - added EXtract FIeld
931201 - 1.0 - added EX FOrmat, MUltiple and PRocheck
940415 - 1.1 - improved O2D plot files
960219 - 1.2 - minor bug fix (if too many values in histogram
command, it no longer crashes; also, allow more
values in histogram command)
960301 -1.2.1- cut array dimensioning back so it will run on smaller
machines
960409 - 1.3 - implemented macro facility
960517 - 1.4 - implemented simple symbol mechanism
970616 - 1.5 - implemented BOxcar averaging of real datablocks
970626 - 1.6 - support initialisation macro (setenv GKODBMAN macrofile)
980930 - 1.7 - optional parameter to the SImilarity command, to only
list datablocks for which the correlation coefficient
exceeds a minimum value; new ALl_correlations command
to find sets of datablocks with high correlation
coefficient
981001 - 1.8 - optional parameter max_correlation for the SImilarity
and ALl_correlations commands; new CGraph_file command
to save numeric datablocks in a TAB-delimited file that
can be imported into CricketGraph etc.
981014 -1.8.1- PLot and SCatter files now contain some statistics
about the plotted datablock(s) (ave, sd, min, max;
correlation coefficient and rmsd)
981019 -1.8.2- minor bug fix in the above (min and max were screwed up)
981020 -1.8.3- minor bug fix needed for ALPHAs; also reduced memory
allocation
981021 -1.8.4- new ECho command to echo command-line input (useful
in scripts)
981022 - 1.9 - implemented command history (# command)
981112 -1.9.1- minor bug fixes (REad and CGraph commands)
990303 -1.9.2- minor fix in SImilarity and ALl_correlations options.
The last (optional) parameter for these commands is now
actually used (it may be Table of List and determines
the output format).
From version 1.6 on, ODBMAN can execute a macro at start-up (whether it is run interactively or in batch mode). This can be used to execute commands which you (almost) always want to have executed. To use this feature, set the environment variable GKODBMAN to point to a ODBMAN macro file, e.g.:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- setenv GKODBMAN /home/gerard/odbman.init ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
ODBMAN is a program for manipulating O datablocks (ODBs).
Some of the possibilities:
(1) analysing individual datablocks
(2) simple math operations on datablocks
(3) correlating sets of two datablocks
(4) plotting a single datablock
(5) generating a scatter plot from two datablocks
(6) "translating" datablocks
(7) setting specific values in a datablock
(8) compressing text datablocks
(9) extracting datablocks from ASCII files (e.g., X-PLOR and PROCHECK
output files)
The command interface is similar to the one used by MAMA, MAPMAN, DATAMAN etc. Again, every datablock has a name by which you refer to it. In addition, each datablock has a type, a length and a format.
Name: this must be 25 characters or less; all names are
automatically converted to UPPERCASE.
Type: must be one of Real, Integer, Character or Text;
Character entries may contain up to 6 characters;
Text entries may contain up to 72 characters
Format: must be appropriate for the type of datablock:
- Real: format must be F, E or G
- Integer: format must be I
- Character: format must be A
- Text: exception: "format" is the number of characters
in each entry (ODBMAN will always reduce this
number so that it is just big enough to contain all
entries)
When referring to datablocks, you have a lot of wildcards available:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- * for all datablocks # for all integer datablocks % for all real datablocks #% or %# for all numerical datablocks $ for all character datablocks @ for all text datablocks $@ or @$ for all character and text datablocks *XYZ* for all datablocks containing "XYZ" *XYZ for all datablocks ending in "XYZ" XYZ* for all datablocks beginning with "XYZ" ? for this list ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that the only thing that is not allowed is using embedded
asterisks (i.e., you cannot type *9*residue*).
Many ODBMAN commands allow you to use all of these wildcards;
this is indicated by "odb*" in the list of commands that you
get when you type a single question mark.
Others are more restricted. For example, the SImilarity command
must have ONE Real OR Integer datablock as its first argument
(indicated by "RI_odb" in the list of commands), and one OR
more Real and/or Integer datablocks as its second argument.
So, here you could type "simil m9a_residue_rsfit #%", if you
want to look for residue properties which are correlated with
your RS-fit values.
Communication of datablocks between O and ODBMAN is simple:
in O, use things like:
write m9a* m9a.odb
to write all datablocks pertaining to a particular molecule
to a file, and:
read m9a_new.odb
to read ODB files created by ODBMAN.
In ODBMAN you use the same commands to read and write ODBs.
When you start ODBMAN, the program shows you a list of all available commands, their sub-commands (if any) and their parameters (if any). In addition, some information about the array dimensioning is printed:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN ***Version - 981014/1.8.1 (C) 1992-98 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 - Sat Oct 17 01:17:54 1998 User - gerard Mode - interactive Host - sarek ProcID - 9323 Tty - /dev/ttyq17
*** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN ***
Reference(s) for this program:
* 1 * G.J. Kleywegt (1997). Les amis d"O. CCP4/ESF-EACBM Newsletter on Protein Crystallography 34, September 1997, pp. 5-8. [http://alpha2.bmc.uu.se/usf/factory_8.html]
* 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.
==> For manuals and complete references, visit: ==> http://alpha2.bmc.uu.se/usf
*** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN *** ODBMAN ***
Max nr of O data blocks (odb) : ( 200) Total nr of O data blocks : ( 800) Max nr of elements per odb : ( 10000) Max length of text odbs : ( 72)
Symbol PROGRAM : (ODBMAN) Symbol VERSION : (981014/1.8.1) Symbol START_TIME : (Sat Oct 17 01:17:54 1998) Symbol USERNAME : (gerard)
ODBMAN options :
? (list options) ! (comment) QUit $ shell_command & symbol value & ? (list symbols) @ macro_file
REad filename WRite odb* filename DElete odb* TYpe odb* FOrmat RIC_odb* new_format NAme odb new_name CReate name type nr_elements format DUplicate old_odb new_odb
LIst odb* STats RI_odb* HIsto RI_odb* x1 x2 x3 [...] SImilarity RI_odb1 RI_odb2* [min] [max] BOxcar R_odb* window_size ALl_correlations [min] [max]
PLot_file RI_odb file [y_lo y_hi label_x label-y] SCatter RI_odb1 RI_odb2 file [label_x label_y] CGraph_file RI_odb* file
CHaracter_function CT_odb function INteger_func I_odb function value FLoat_func R_odb function value
SEt ALl odb value SEt MAny odb first last value SEt INdiv odb first last [values] SEt ONe odb index value SEt IF odb other_odb operator value SEt KEep odb first last [step]
EXtract FIeld odb type file head_skip line_skip field_nr EXtract FOrmat odb type file head_skip line_skip format EXtract MUltiple odb type file head_skip format EXtract PRocheck mol_name file
Max nr of O data blocks (odb) : ( 200) Total nr of O data blocks : ( 800) Max nr of elements per odb : ( 10000) Max length of text odbs : ( 72)
ODBMAN > ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
This command can be used to manipulate symbols. These are probably
only useful for advanced users who want to write fancier macros.
The command can be used in three ways:
(1) & ? -> lists currently defined symbols
(2) & symbol value -> sets "SYMBOL" to "value"
(3) & symbol -> prompts the user to supply a value for "SYMBOL"
(even if the program is executing a macro)
A few symbols are predefined:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > & ? Nr of defined symbols : ( 4) Symbol PROGRAM : (ODBMAN) Symbol VERSION : (960517/1.4) Symbol START_TIME : (Fri May 17 20:37:24 1996) Symbol USERNAME : (gerard) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The symbol mechanism is fairly simplistic and has some limitations:
- max length of a symbol name is 20 characters
- max length of a symbol value is 80 characters
- max number of symbols is 100
- symbols can not be deleted, but they can be redefined
- symbol values are accessed by supplying $SYMBOL_NAME as an
argument on the command line; the line that you type on the terminal
(or in a macro) is parsed once; if there are additional parameters
which the program prompts you for, you cannot use symbols for those
- only one substitution per argument (e.g., "$file1 $file2" will
lead to a substituion of the entire argument by the value of
symbol FILE1 only !)
- command names (first argument on any command line) cannot be
replaced by a symbol (e.g.: "$command $arg1 $arg2" is not valid)
- symbols may be equated to each other, e.g. "& file2 $file1" will
give FILE2 the same value as FILE1
- symbol substitution is not recursive (e.g., if you set the value
of FILE2 to be "$file1", any reference to $FILE2 will be replaced
by "$file1", not by the value of FILE1
- symbols on comment lines (starting with "!") are not expanded
- symbols on system command lines (starting with "$") are not expanded
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > re q.odb Created by ODBMAN V. 931129/0.4 at Mon Nov 29 22:09:42 1993 for user gerard Read : (M9A_ATOM_XYZ R 3843 (10(X,F7.4))) Read : (M9A_ATOM_B R 1281 (10(X,F7.3))) Read : (M9A_ATOM_WT R 1281 (10(X,F7.5))) Read : (M9A_RESIDUE_CG R 636 (10(X,F7.4))) Read : (M9A_CELL R 6 (8(X,F8.4))) ... Read : (M9A_SPACEGROUP T 1 1) Read : (M9A_DATE T 1 24) Nr of datablocks read : ( 29) Nr of header/comments : ( 30) Datablock read okay ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > li *residue*Datablock name Type Nr Alt? Format M9A_RESIDUE_CG R 636 F (10(X,F7.4)) M9A_RESIDUE_PEPFLIP R 159 F (10(X,F7.5)) M9A_RESIDUE_RSC R 159 F (10(X,F7.4)) M9A_RESIDUE_MC_B R 159 F (10(X,F7.3)) M9A_RESIDUE_RSFIT R 159 F (10(X,F7.5)) M9A_RESIDUE_POINTERS I 318 F (16(X,I4)) M9A_RESIDUE_PIECES I 159 F (40(X,I1)) M9A_RESIDUE_CA_IDX I 159 F (16(X,I4)) M9A_RESIDUE_NAME C 159 F (12(1X,A6)) M9A_RESIDUE_TYPE C 159 F (12(1X,A6)) M9A_RESIDUE_2RY_STRUC C 159 F (12(1X,A6)) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > del *pointers Delete : (*POINTERS) Sure (Y/N) ? (N) y Deleting : (M9A_RESIDUE_POINTERS) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > wr *residue* res.odb Written : (M9A_RESIDUE_CG R 636 (10(X,F7.4))) Written : (M9A_RESIDUE_PEPFLIP R 159 (10(X,F7.5))) Written : (M9A_RESIDUE_RSC R 159 (10(X,F7.4))) Written : (M9A_RESIDUE_MC_B R 159 (10(X,F7.3))) Written : (M9A_RESIDUE_RSFIT R 159 (10(X,F7.5))) Written : (M9A_RESIDUE_PIECES I 159 (40(X,I1))) Written : (M9A_RESIDUE_CA_IDX I 159 (16(X,I4))) Written : (M9A_RESIDUE_NAME C 159 (12(1X,A6))) Written : (M9A_RESIDUE_TYPE C 159 (12(1X,A6))) Written : (M9A_RESIDUE_2RY_STRUC C 159 (12(1X,A6))) Nr of datablocks written : ( 10) Datablock write okay ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
ODBMAN > ty M9A_RESIDUE_2RY_STRUC
M9A_RESIDUE_2RY_STRUC C 159 (12(1X,A6))
BETA BETA BETA ALPHA ALPHA ALPHA BETA BETA BETA
BETA BETA BETA BETA BETA
BETA BETA ALPHA ALPHA ALPHA
BETA BETA BETA BETA BETA BETA BETA BETA BETA
BETA BETA BETA BETA BETA BETA BETA BETA
BETA BETA BETA BETA BETA BETA BETA BETA BETA BETA
BETA BETA BETA BETA BETA BETA
BETA BETA BETA BETA BETA
BETA BETA BETA BETA BETA BETA BETA BETA BETA
BETA BETA BETA BETA BETA BETA BETA BETA BETA BETA
BETA ALPHA ALPHA ALPHA ALPHA ALPHA
ALPHA ALPHA ALPHA ALPHA ALPHA ALPHA ALPHA ALPHA ALPHA
ALPHA ALPHA ALPHA BETA BETA BETA BETA
Nr of datablocks written : ( 1)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > form $ (10(1x,a6)) New Character format : ((10(1X,A6))) Processing : (M9A_RESIDUE_NAME) Processing : (M9A_RESIDUE_TYPE) Processing : (M9A_ATOM_NAME) Processing : (M9A_MOLECULE_TYPE) Processing : (M9A_MOLECULE_CA) Processing : (M9A_RESIDUE_2RY_STRUC) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > name M9A_RESIDUE_2RY_STRUC m10a_residue_2ry_struc Old name : (M9A_RESIDUE_2RY_STRUC) New name : (M10A_RESIDUE_2RY_STRUC) ODBMAN > list *2ry*Datablock name Type Nr Alt? Format M10A_RESIDUE_2RY_STRUC C 159 T (10(1X,A6)) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > stats *flipStats : (M9A_RESIDUE_PEPFLIP) Nr of elements : ( 159) Minimum : ( 0.000E+00) Maximum : ( 2.814E+00) Sum : ( 1.231E+02) Average : ( 7.739E-01) St-devn : ( 5.519E-01) Variance : ( 3.046E-01) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > box % 7 Box-car average : (M8A_MOLECULE_CA_MXDST) Box-car average : (M8A_SYMMOP) Box-car average : (M8A_RESIDUE_RSC) Box-car average : (M8A_RESIDUE_PEPFLIP) Box-car average : (M8A_RESIDUE_GEOMPLOT) Box-car average : (M8A_ATOM_XYZ) Box-car average : (M8A_ATOM_B) Box-car average : (M8A_ATOM_WT) Box-car average : (M8A_RESIDUE_CG) Box-car average : (M8A_CELL) Box-car average : (M8A_PDB_SCALE) Box-car average : (M8A_RESIDUE_RSFIT) Box-car average : (M8A_RESIDUE_HBOND) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > hist m9a_residue_rsfit 0.0 0.4 0.6 0.8 Histrogram limits : ( 0.000E+00 4.000E-01 6.000E-01 8.000E-01)Histogram : (M9A_RESIDUE_RSFIT)
Nr < 0.0000 : 0 ( 0.00 %; Cum 0.00 %) Nr >= 0.4000 and < 0.6000 : 5 ( 3.14 %; Cum 3.14 %) Nr >= 0.6000 and < 0.8000 : 51 ( 32.08 %; Cum 35.22 %) Nr >= 0.8000 : 103 ( 64.78 %; Cum 100.00 %) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > plot m9a_residue_pepflip m9a_flip.plt 0 3.5 "residue number" "pep-flip value" Y lower : ( 0.000E+00) Y upper : ( 3.500E+00) X label : (residue number) Y label : (pep-flip value) O2D plot file written ODBMAN > $ cat m9a_flip.plt ! Created by ODBMAN V. 931129/0.4 at Mon Nov 29 23:00:01 1993 for user gerard NPOINT 159 XLABEL residue number YLABEL pep-flip value COLOUR 2 XLIMIT 1.0 1.0 XYVIEW 0.0000E+00 1.6000E+02 0.0000E+00 3.5000E+00 YVALUE * 0.0000E+00 0.0000E+00 4.5207E-01 6.4544E-01 4.5521E-01 1.8592E-01 8.8254E-01 7.4481E-01 2.3498E+00 9.1692E-01 8.6838E-01 4.6378E-01 ... 5.5748E-01 4.8489E-01 1.4008E+00 1.0811E+00 7.8445E-01 2.0441E+00 0.0000E+00 0.0000E+00 0.0000E+00 END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > sim M9A_RESIDUE_RSfit %Comparing : (M9A_RESIDUE_RSFIT) And : (M9A_RESIDUE_PEPFLIP) Nr of elements : ( 159) RMS difference: ( 5.684E-01) Correl Coeff : ( -0.116) Shape Similarity : ( 0.803) R-factor (1) : ( 5.235E-01) Ditto, 2 scaled : ( 0.530) Scale for 2 : ( 1.042) R-factor (2) : ( 5.453E-01) Ditto, 1 scaled : ( 0.530) Scale for 1 : ( 0.960) ... Comparing : (M9A_RESIDUE_RSFIT) And : (M9A_RESIDUE_MC_B) Nr of elements : ( 159) RMS difference: ( 3.541E+01) Correl Coeff : ( -0.739) Shape Similarity : ( 0.832) R-factor (1) : ( 3.811E+01) Ditto, 2 scaled : ( 0.468) Scale for 2 : ( 0.026) R-factor (2) : ( 9.747E-01) Ditto, 1 scaled : ( 0.468) Scale for 1 : ( 39.103) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > all 0.999 Minimum correlation coefficient : ( 0.999)Comparing : (INPUT_RANDOM_DELETE_PERC) And : (SNAFU_REJ_RANDOM) Nr of elements : ( 25) Correl Coeff : ( 1.000) RMS difference : ( 1.062E+04) Shape Similarity : ( 1.000) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > sc M9A_RESIDUE_RSFIT M9A_RESIDUE_MC_B rsfit_b.plt "rs-fit all atoms" "main-chain B" X label : (rs-fit all atoms) Y label : (main-chain B) X lower : ( 5.052E-01) X upper : ( 9.362E-01) Y lower : ( -6.254E+00) Y upper : ( 1.313E+02) O2D plot file written ODBMAN > $ cat rsfit_b.plt ! Created by ODBMAN V. 931129/0.4 at Mon Nov 29 23:15:32 1993 for user gerard NPOINT 159 XLABEL rs-fit all atoms YLABEL main-chain B COLOUR 3 XYVIEW 5.0519E-01 9.3618E-01 -6.2545E+00 1.3134E+02 XVALUE * 5.2478E-01 6.9678E-01 8.1501E-01 7.0230E-01 7.9696E-01 7.1953E-01 5.3427E-01 6.2648E-01 6.1243E-01 7.3070E-01 7.3338E-01 8.0263E-01 ... 7.9396E-01 6.0540E-01 5.9415E-01 YVALUE * 9.0280E+01 7.4600E+01 4.9620E+01 4.6760E+01 5.1480E+01 6.1710E+01 ... 3.7800E+01 1.2509E+02 0.0000E+00 END ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > cg % snafu.cg Nr of datablocks selected : ( 134) Max nr of elements : ( 40) CricketGraph file written CPU total/user/sys : 15.8 15.8 0.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Note that only real and integer datablocks will be written:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > list m8a_resi*Datablock name Type Nr Alt? Format M8A_RESIDUE_RSC R 262 F (10(X,F7.4)) M8A_RESIDUE_PEPFLIP R 262 F (10(X,F7.5)) M8A_RESIDUE_GEOMPLOT R 262 F (10(X,F7.4)) M8A_RESIDUE_RSFIT R 262 F (10(X,F7.5)) M8A_RESIDUE_HBOND R 262 F (8(X,F8.5)) M8A_RESIDUE_BADCOUNTS I 262 F (40(X,I1)) M8A_RESIDUE_BADCON I 262 F (40(X,I1)) M8A_RESIDUE_NAME C 262 F (1X,5A) M8A_RESIDUE_TYPE C 262 F (1X,5A) M8A_RESIDUE_DSSP C 262 F (1X,5A) M8A_RESIDUE_RAMA C 262 F (1X,5A) ODBMAN > cg m8a_resi* fcpg.cg Nr of datablocks selected : ( 7) Max nr of elements : ( 262) CricketGraph file written CPU total/user/sys : 6.0 6.0 0.0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
UP - converts the entries to UPPERCASE
LO - converts them to lowercase
PR - replaces multiple spaces by a single space
RE - removes all spaces
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > ch $ ? Available character functions : UPpercase LOwercase PRetty REmove_spacesODBMAN > ch $ up Character function : (UP) Processing : (M9A_RESIDUE_NAME) Processing : (M9A_RESIDUE_TYPE) Processing : (M9A_ATOM_NAME) Processing : (M9A_MOLECULE_TYPE) Processing : (M9A_MOLECULE_CA) Processing : (M10A_RESIDUE_2RY_STRUC) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
LO - applies: value(i) = max(value(i), new_lower_bound)
HI - applies: value(i) = min(value(i), new_upper_bound)
AD - add a constant to all values
MU - multiply all values by a constant
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > in # ? Available integer functions : LOwer_bound_reset UPper_bound_reset ADd MUltiplyODBMAN > in M9A_ATOM_COLOUR mu 2 Integer function : (MU) Value : ( 2) Processing : (M9A_ATOM_COLOUR) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
LO - applies: value(i) = max(value(i), new_lower_bound)
HI - applies: value(i) = min(value(i), new_upper_bound)
AD - add a constant to all values
MU - multiply all values by a constant
IN - removes everything behind the decimal point (3.74 -> 3)
NE - replaces every entry by the nearest integer (3.74 -> 4)
SQ - replaces each entry by its square root
PO - raises each entry to a power
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > fl % ? Available floating point functions : LOwer_bound_reset UPper_bound_reset ADd MUltiply INteger_cutoff NEarest_integer SQuare_root POwer_raiseODBMAN > fl M9A_ATOM_B lo 5 Floating point function : (LO) Value : ( 5.000E+00) Processing : (M9A_ATOM_B) ODBMAN > fl M9A_ATOM_B up 50 Floating point function : (UP) Value : ( 5.000E+01) Processing : (M9A_ATOM_B) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > cre m9a_residue_yasspa Type (R/I/C/T) ? (C) i Number of elements ? (1) 159 Format ? ((6I12)) (35i2) Initialised new odb : (M9A_RESIDUE_YASSPA) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > dup M9A_ATOM_XYZ M9A_ATOM_XCOORD Duplicate odb : (M9A_ATOM_XCOORD) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The SET commands can be used to set one or more values in a particular datablock. The commands handle any type of datablock.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > set all m9a_residue_yasspa 0 ODBMAN > ty m9a_residue_yasspa M9A_RESIDUE_YASSPA I 159 (35I2) 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Nr of datablocks written : ( 1) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > set many m9a_residue_yasspa 10 16 1 ODBMAN > ty m9a_residue_yasspa M9A_RESIDUE_YASSPA I 159 (35I2) 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Nr of datablocks written : ( 1) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > set ind m9a_residue_yasspa 15 21 Entries 15 - 18 ? ( 1 1 0 0) 1 1 0 2 Entries 19 - 21 ? ( 0 0 0) 2 2 ODBMAN > ty m9a_residue_yasspa M9A_RESIDUE_YASSPA I 159 (35I2) 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 0 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Nr of datablocks written : ( 1) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > set one m9a_residue_yasspa 19 4 ODBMAN > ty m9a_residue_yasspa M9A_RESIDUE_YASSPA I 159 (35I2) 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 0 2 4 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Nr of datablocks written : ( 1) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > create m9a_residue_yasspa i 159 (40i2) Initialised new odb : (M9A_RESIDUE_YASSPA) ODBMAN > set if m9a_residue_yasspa 1 M9A_RESIDUE_2RY_STRUC = ALPHA Entries set : ( 23) Out of : ( 159) ODBMAN > set if m9a_residue_yasspa -1 M9A_RESIDUE_2RY_STRUC = BETA Entries set : ( 75) Out of : ( 159) ODBMAN > ty m9a_residue_yasspa M9A_RESIDUE_YASSPA I 159 (40I2) 0-1-1-1 1 1 1 0 0-1-1-1 0 0 0 0 0-1-1-1 0 0-1-1-1-1 0 0 0 1 1 1 0 0 0 0 0 0 0-1 -1-1-1-1-1-1-1-1 0 0-1-1-1-1-1-1-1-1 0 0 0 0-1-1-1-1-1-1-1-1-1-1-1 0 0 0 0 0-1-1 -1-1-1 0 0 0-1-1-1-1-1 0 0 0 0 0 0 0 0-1-1-1-1-1-1-1-1-1-1 0 0-1-1-1-1-1-1-1-1-1 -1 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 1 1 1-1-1-1-1 0 0 0 0 0 0 0 0 Nr of datablocks written : ( 1) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The parameters are:
- the name of the datablock in which values must be set
- the value to be set IF the following condition is true
- the comparison datablock
- the operator (=, <, > or #, not-equal-to)
- the comparison value
In the example above we typed:
set if m9a_residue_yasspa -1 M9A_RESIDUE_2RY_STRUC = BETA
this means: set each entry in ODB m9a_residue_yasspa to -1,
IF the value of the corresponding entry in M9A_RESIDUE_2RY_STRUC
is equal to the string BETA (otherwise, the value is NOT
affected).
The following example is "a poor man's implementation of OOPS" (in O, you could use centre_next to go from one suspicious residue to the next):
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > create m9a_residue_quality c 159 Format ? ((14A6)) Initialised new odb : (M9A_RESIDUE_QUALITY) ODBMAN > set all m9a_residue_quality GOOD ODBMAN > set if m9a_residue_quality BAD m9a_residue_rsfit < 0.6 Entries set : ( 5) Out of : ( 159) ODBMAN > set if m9a_residue_quality BAD m9a_residue_pepflip > 2.5 Entries set : ( 3) Out of : ( 159) ODBMAN > set if m9a_residue_quality BAD m9a_residue_rsc > 1.5 Entries set : ( 20) Out of : ( 159) ODBMAN > ty m9a_residue_quality M9A_RESIDUE_QUALITY C 159 (14A6) BAD GOOD GOOD GOOD GOOD GOOD BAD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD BAD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD BAD BAD GOOD BAD GOOD GOOD GOOD BAD GOOD GOOD GOOD BAD GOOD GOOD GOOD BAD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD BAD GOOD GOOD GOOD GOOD GOOD BAD GOOD GOOD GOOD GOOD GOOD GOOD BAD GOOD GOOD BAD BAD GOOD GOOD GOOD GOOD BAD BAD GOOD BAD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD BAD GOOD GOOD GOOD GOOD GOOD BAD GOOD GOOD GOOD BAD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD BAD GOOD BAD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD BAD GOOD GOOD GOOD BAD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD GOOD BAD BAD Nr of datablocks written : ( 1) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
- cutting out specific bits of a datablock: e.g., if you just want to plot the RS-fit values for one molecule (or only for your water molecules), you could use DUPLICATE to get a copy of the RS-fit datablock, and then cut out the appropriate bit(s) from this datablock:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > dupl M9A_RESIDUE_RSFIT water_residue_rsfit Duplicate odb : (WATER_RESIDUE_RSFIT) ODBMAN > set keep water_residue_rsfit 128 99999 1 Nr of entries before : ( 159) Nr of entries after : ( 32) ODBMAN > ty water_residue_rsfit WATER_RESIDUE_RSFIT R 32 (10(X,F7.5)) 0.78577 0.70488 0.78062 0.80997 0.74287 0.73245 0.80670 0.86725 0.76592 0.72771 0.77582 0.76987 0.77744 0.83253 0.83447 0.81540 0.78326 0.75658 0.66148 0.79989 0.81657 0.79834 0.81534 0.79682 0.81085 0.64254 0.71165 0.68426 0.64383 0.79396 0.60540 0.59415 Nr of datablocks written : ( 1) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
- collapsing a datablock: this is actually why I wrote this option. Suppose you want to colour your protein in the colours of the Dutch flag. In that case, you could colour your molecule depending on the X-coordinate of each atom. In order to do that, you want to have a datablock which for each atom contains only its X-coordinate, which means keeping only every third value, starting at the first one:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > dupl M9A_ATOM_XYZ M9A_ATOM_XCOORD Duplicate odb : (M9A_ATOM_XCOORD) ODBMAN > set keep M9A_ATOM_XCOORD 1 100000 3 Nr of entries before : ( 3843) Nr of entries after : ( 1281) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
You must supply:
- the name of the new datablock
- its type (Real or Integer)
- the name of the file which is to be scanned
- the number of lines to skip at the top of the file (0, 1, ...)
- the number of lines to skip after an item has been read
from a line (0, 1, ...)
- the number of the field on a line in the file which is to
be read; fields are items on a line separated by spaces
(unless these spaces occur within "double quotes")
For example, suppose we have an output file from an X-PLOR PC-refinement job and we want to extract the final PC values. The file typically looks as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 450 gerard rigel 22:00:46 progs/odbman > cat q.list 263.44 42.5 118.05 263.36 39.305 119.72 1 3.5624 4.89073E-02 8.68781E-02 9.80972E-02 133.01 60 133.01 133.94 59.77 132.86 3 3.5403 4.73586E-02 7.79348E-02 8.33885E-02 286.18 40 95.156 287.26 39.678 93.268 14 3.5095 6.54724E-02 9.34291E-02 9.42023E-02 133.6 55 144.51 133.94 54.367 144.43 26 3.4889 4.62323E-02 8.35917E-02 8.95851E-02 246.69 50 114.69 248.44 49.442 115.26 65 3.4343 5.73853E-02 8.61116E-02 9.02212E-02 107.06 45 355.79 103.92 44.396 359.08 177 3.3305 5.04327E-02 7.59372E-02 8.4106E-02 127.77 55 127.77 130.21 55.843 124.69 201 3.321 5.18844E-02 8.66048E-02 0.10473 260.69 45 110.14 261.86 44.921 112.42 350 3.2369 4.31585E-02 9.56762E-02 0.10101 97.595 42.5 353.75 93.937 42.84 357.25 432 3.2022 4.8324E-02 8.43962E-02 9.00757E-02 279.16 40 110.18 278.15 35.811 110.15 487 3.1745 4.39592E-02 8.06346E-02 9.39514E-02 123.99 52.5 141.13 121.87 51.767 144.7 496 3.1718 3.49398E-02 7.19334E-02 9.45314E-02 236.47 55 116.47 233.35 55.397 118.42 591 3.1326 4.17005E-02 9.50638E-02 0.1025 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
In this case, we don't need to skip any lines and we want to extract the last, that is the eleventh, item from each line:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
ODBMAN > ex fi pc_ref r q.list 0 0 11
Number of lines read : ( 12)
Number of values read : ( 12)
Extracted new odb : (PC_REF)
ODBMAN > ty pc_ref
PC_REF R 12 (5E14.4)
0.9810E-01 0.8339E-01 0.9420E-01 0.8959E-01 0.9022E-01
0.8411E-01 0.1047E+00 0.1010E+00 0.9008E-01 0.9395E-01
0.9453E-01 0.1025E+00
Nr of datablocks written : ( 1)
ODBMAN > st pc_ref
Stats : (PC_REF)
Nr of elements : ( 12)
Minimum : ( 8.339E-02)
Maximum : ( 1.047E-01)
Sum : ( 1.126E+00)
Average : ( 9.387E-02)
St-devn : ( 6.539E-03)
Variance : ( 4.276E-05)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Useful combinations of numbers for some file types are:
X-PLOR xxx.rf , use: 1 0 5
X-PLOR filter.list , use: 0 0 11
X-PLOR search.dat , use: 0 0 4
X-PLOR geomplot.list, use: 0 0 2
You must supply:
- the name of the new datablock
- its type (Real or Integer)
- the name of the file which is to be scanned
- the number of lines to skip at the top of the file (0, 1, ...)
- the number of lines to skip after an item has been read
from a line (0, 1, ...)
- the format for reading ONE item from ONE line, for example
(10x,f8.3) or (56x,i4)
For example, suppose we have an output file from an X-PLOR combined translation function job and we want to extract the TF values (e.g., in order to plot them). The file typically looks as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
(* Translation Function *)
rnumber= 240;
rave= 0.099;
rsigma= 0.008;
rmax= 0.119;
rmin= 0.084;
var={ "x", "y", "z" };
min={ 0.00000 , 0.00000 , 0.00000 };
max={ 0.00000 , 1.00000 , 0.00000 };
rf={
{
{
0.1066
},
{
0.1080
...
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
So, what we need to do is: to skip 12 lines of the header, read a Real number in format (f11.4) [or (f20.1), it doesn't matter since in this particular case there's only one number per line], and then skip two more lines:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > ex form ctf r c.3dm 12 2 (f11.4) ERROR --- Unexpected error reading item from line Number of lines read : ( 733) Number of values read : ( 240) Extracted new odb : (CTF) ODBMAN > st ctfStats : (CTF) Nr of elements : ( 240) Minimum : ( 8.360E-02) Maximum : ( 1.186E-01) Sum : ( 2.374E+01) Average : ( 9.893E-02) St-devn : ( 8.217E-03) Variance : ( 6.752E-05) ODBMAN > li ctf
Datablock name Type Nr Alt? Format CTF R 240 T (5E14.4) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
There occurs a read error at the end of the file, since the last line contains " }; ", but you don't need to worry about that. Note that 3*240 + 12 (header) + 1 (last line) = 733 indeed.
Another example: if Gert Vriend has run his Direct Atomic Contact Analysis program, you may want to analyse and plot the values on a per-residue basis. Edit the file so it only contains the listing of values:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
1 GLU (5 ) : -2.640
2 GLU (6 ) : -1.849
3 ALA (7 ) : 1.643
4 SER (8 ) : 1.958
5 SER (9 ) : -0.837
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Then extract the values as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- ODBMAN > ex form gerard_residue_daca r gerard.daca 0 0 (20x,f8.3) Number of lines read : ( 628) Number of values read : ( 628) Extracted new odb : (GERARD_RESIDUE_DACA) CPU total/user/sys : 1.5 1.4 0.2 ODBMAN > st GERARD_RESIDUE_DACAStats : (GERARD_RESIDUE_DACA) Nr of elements : ( 628) Minimum : ( -5.444E+00) Maximum : ( 7.201E+00) Sum : ( 7.998E+00) Average : ( 1.274E-02) St-devn : ( 2.534E+00) Variance : ( 6.421E+00) ODBMAN > plot gerard_residue_daca gerard_daca.plt -8 8 "Residue" "DACA value" Y lower : ( -8.000E+00) Y upper : ( 8.000E+00) X label : (Residue) Y label : (DACA value) O2D plot file written ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
You must supply:
- the name of the new datablock
- its type (Real or Integer)
- the name of the file which is to be scanned
- the number of lines to skip at the top of the file (0, 1, ...)
- the format for reading ALL items, for example
(8f6.2) or (28x,3f8.3//)
You could use this option, for example, to read coordinates
from a PDB file, to read an ODB file, or to extract phi/psi
angle combinations from a program which produces a list of
these.
With this option you should always check whether the last
entry in the new datablock is genuine, or whether it has
a bogus value of zero (if so, use SET KEEP to get rid of it).
- xxx_residue_type (C)
- xxx_residue_name (C)
- xxx_residue_dssp (C) = secondary structure assignment
- xxx_residue_rama (C) = area of the Ramachandran plot
- xxx_residue_badcon (I) = number of bad contacts
- xxx_residue_hbond (R) = H-bond energy
If a datablock with the same name already exists, it is NOT
overwritten ! The "mol_name" which you provide as the first
parameter to this command will replace the "xxx" in the names
of the ODBs listed above.
Note that the DSSP and RAMA datablocks have been converted to
uppercase !
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
ODBMAN > ex pro m7a m7a.out
Start of residue listing; extracting
1 PRO A1 - 1 0.0
2 SER A2 XX 0 -2.0
3 VAL A3 XX 0 0.0
4 PHE A4 E B 0 -1.9
5 LEU A5 E B 0 0.0
...
260 VAL A453 E B 0 -2.3
261 THR A454 E B 1 -1.3
262 GLU A455 E - 0 -1.7
End of residue listing; skip rest of file
Nr of lines read : ( 561)
All done !
ODBMAN > li *
Datablock name Type Nr Alt? Format
M7A_RESIDUE_HBOND R 262 T (1x,15f5.1)
M7A_RESIDUE_BADCON I 262 T (1x,25i3)
M7A_RESIDUE_TYPE C 262 T (1x,5a)
M7A_RESIDUE_NAME C 262 T (1x,5a)
M7A_RESIDUE_DSSP C 262 T (1x,5a)
M7A_RESIDUE_RAMA C 262 T (1x,5a)
ODBMAN > st %#
Stats : (M7A_RESIDUE_HBOND)
Nr of elements : ( 262)
Minimum : ( -3.800E+00)
Maximum : ( 0.000E+00)
Sum : ( -2.368E+02)
Average : ( -9.038E-01)
St-devn : ( 9.701E-01)
Variance : ( 9.411E-01)
Stats : (M7A_RESIDUE_BADCON)
Nr of elements : ( 262)
Minimum : ( 0.000E+00)
Maximum : ( 1.000E+00)
Sum : ( 1.000E+01)
Average : ( 3.817E-02)
St-devn : ( 1.916E-01)
Variance : ( 3.671E-02)
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If you read these datablocks into O, you can use them to colour your molecule, for example:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- O > mol m7a pai_zo m7a a1 a262 yellow O > pai_case residue_dssp 5 e h t s g green red blue magenta cyan O > obj dssp ca ; end ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- O > pai_zo m7a a1 a262 green O > pai_case residue_rama 5 ~a ~b ~l ~p xx yellow yellow yellow yellow red O > obj rama ca ; end ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- O > pai_ramp residue_badcon ; blue red O > obj badcon ca ; end ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- O > pa_zo m7a a1 a262 green O > pai_prop residue_hbond < -4 red O > pai_prop residue_hbond > 0 yellow O > obj hbond ca ; end ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
None, at present.
Created at Wed Mar 10 23:31:05 1999
by MAN2HTML version 971024/1.6