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contacts |
Contact between two residues is defined as when the van der Waals surface of any atom of the first residue comes within the threshold contact distance of the van der Waals surface of any atom of the second residue. The threshold contact distance is a user-defined distance with a default value of 1 Angstrom.
The following van der Waals radii are used:
C:1.8 Angstrom O:1.4 Angstrom N:1.7 Angstrom S:2.0 Angstrom H:1.0 Angstrom (default for other or unknown atom types)
% contacts Reads coordinate files and writes contact files Location of coordinate files for input (embl-like format) [./]: Extension of coordinate files (embl-like format) [.pxyz]: Location of contact files for output [./]: Extension of contact files [.con]: Threshold contact distance [1.0]: Name of data file with van der Waals radii [Evdw.dat]: Name of log file for the build [contacts.log]:
Mandatory qualifiers: [-cpdb] string Location of coordinate files (embl format input) [-cpdbextn] string Extension of coordinate files -vdwf string Name of data file with van der Waals radii -thresh float Threshold contact distance [-con] string Location of contact files for output [-conextn] string Extension of contact files -conerrf outfile Name of log file for the build Optional qualifiers: (none) Advanced qualifiers: -ignore float If any two atoms from two different residues are at least this distance apart then no futher inter-atomic contacts will be checked for for that residue pair . This speeds the calculation up considerably. General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-cpdb] (Parameter 1) |
Location of coordinate files (embl format input) | Any string is accepted | ./ |
[-cpdbextn] (Parameter 2) |
Extension of coordinate files | Any string is accepted | .pxyz |
-vdwf | Name of data file with van der Waals radii | Any string is accepted | Evdw.dat |
-thresh | Threshold contact distance | Any numeric value | 1.0 |
[-con] (Parameter 3) |
Location of contact files for output | Any string is accepted | ./ |
[-conextn] (Parameter 4) |
Extension of contact files | Any string is accepted | .con |
-conerrf | Name of log file for the build | Output file | contacts.log |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-ignore | If any two atoms from two different residues are at least this distance apart then no futher inter-atomic contacts will be checked for for that residue pair . This speeds the calculation up considerably. | Any numeric value | 20.0 |
For example:
ID D1HBBA_ XX DE Co-ordinates for SCOP domain D1HBBA_ XX OS See Escop.dat for domain classification XX EX METHOD xray; RESO 1.90; NMOD 1; NCHA 1; XX CN [1] XX IN ID A; NR 141; NH 0; NW 0; XX SQ SEQUENCE 141 AA; 15127 MW; 5EC7DB1E CRC32; VLSPADKTNV KAAWGKVGAH AGEYGAEALE RMFLSFPTTK TYFPHFDLSH GSAQVKGHGK KVADALTNAV AHVDDMPNAL SALSDLHAHK LRVDPVNFKL LSHCLLVTLA AHLPAEFTPA VHASLDKFLA SVSTVLTSKY R XX CO 1 1 P 1 1 V VAL N 7.155 17.725 4.424 1.00 37.82 CO 1 1 P 1 1 V VAL CA 7.854 18.800 3.718 1.00 35.10 CO 1 1 P 1 1 V VAL C 9.366 18.565 3.754 1.00 31.92 CO 1 1 P 1 1 V VAL O 9.861 17.961 4.721 1.00 35.01 CO 1 1 P 1 1 V VAL CB 7.529 20.168 4.360 1.00 47.63 CO 1 1 P 1 1 V VAL CG1 7.806 21.300 3.369 1.00 62.84 CO 1 1 P 1 1 V VAL CG2 6.136 20.244 4.936 1.00 54.85 CO 1 1 P 2 2 L LEU N 10.032 19.062 2.731 1.00 27.38 CO 1 1 P 2 2 L LEU CA 11.496 18.967 2.657 1.00 23.24 CO 1 1 P 2 2 L LEU C 12.077 20.110 3.496 1.00 22.99 CO 1 1 P 2 2 L LEU O 11.672 21.259 3.289 1.00 25.22
Note - SM records are used for contacts between either either side-chain or main-chain atoms as defined above. In a future implementation, SS will be used for side-chain only contacts, MM will be used for main-chain only contacts, and there will probably be several other forms of contact too.
Example contacts output file:
ID D1HBBB_ XX DE Residue-residue side-chain contact data XX EX THRESH 10.0; NMOD 1; NCHA 1; XX MO [1] XX CN [1] XX IN ID B; NR 146; NSMCON 2514; XX SM VAL 1 ; HIS 2 SM VAL 1 ; LEU 3 SM VAL 1 ; THR 4 SM VAL 1 ; PRO 5 SM VAL 1 ; GLU 6 SM VAL 1 ; GLU 7 SM VAL 1 ; LYS 8 SM VAL 1 ; VAL 11 SM VAL 1 ; PHE 71 //
contacts generates a log file an excerpt of which is shown below. If there is a problem in processing a coordinate file, three lines containing the record '//', the scop domain or pdb identifier code and an error message respectively are written. The text 'WARN file open error filename', 'ERROR file read error filename' or 'ERROR file write error filename ' will be reported when an error was encountered during a file open, read or write respectively. Various other error messages may also be given (in case of difficulty email Jon Ison, jison@hgmp.mrc.ac.uk).
Example log file
// DS002__ WARN Could not open for reading cpdb file s002.pxyz // DS003__ WARN Could not open for reading cpdb file s003.pxyz
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.
To see the available EMBOSS data files, run:
% embossdata -showall
To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:
% embossdata -fetch -file Exxx.dat
Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".
The directories are searched in the following order:
Program name | Description |
---|---|
dichet | Parse dictionary of heterogen groups |
hmmgen | Generates a hidden Markov model for each alignment in a directory |
interface | Reads coordinate files and writes files of inter-chain residue-residue contact data |
profgen | Generates various profiles for each alignment in a directory |
psiblasts | Runs PSI-BLAST given scopalign alignments |
scopalign | Generate alignments for families in a scop classification file by using STAMP |
scoprep | Reorder scop classificaiton file so that the representative structure of each family is given first |
scopreso | Removes low resolution domains from a scop classification file |
seqalign | Generate extended alignments for families in a scop families file by using CLUSTALW with seed alignments |
seqsearch | Generate files of hits for families in a scop classification file by using PSI-BLAST with seed alignments |
seqsort | Reads multiple files of hits and writes a non-ambiguous file of hits (scop families file) plus a validation file |
seqwords | Generate file of hits for scop families by searching swissprot with keywords |
siggen | Generates a sparse protein signature from an alignment and residue contact data |
sigscan | Scans a signature against swissprot and writes a signature hits files |