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Difference between revisions of "contact.pl"
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different structures. Residues are considered in contact when the minimum | different structures. Residues are considered in contact when the minimum | ||
inter-residue distance of all pairs of heavy atoms is less than | inter-residue distance of all pairs of heavy atoms is less than | ||
| − | 4. | + | 4.2 Å.<BR> |
| + | |||
In the default mode with two structures as arguments the fraction of contacts | In the default mode with two structures as arguments the fraction of contacts | ||
present in the second structure with respect to the first is determined. | present in the second structure with respect to the first is determined. | ||
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as well as the test structures. | as well as the test structures. | ||
<BR> | <BR> | ||
| + | |||
If only one structure is given as an argument no comparison is done. A residue | If only one structure is given as an argument no comparison is done. A residue | ||
contact list is printed out instead. This list can be used in later comparisons | contact list is printed out instead. This list can be used in later comparisons | ||
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has to be done only once. | has to be done only once. | ||
<BR> | <BR> | ||
| + | |||
The option <B>-l</B> is available to limit the residue map to contacts with | The option <B>-l</B> is available to limit the residue map to contacts with | ||
a subset of residues as might be useful for loop modeling. | a subset of residues as might be useful for loop modeling. | ||
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; -help : usage information | ; -help : usage information | ||
| − | + | ; -l min:max[...] : restrict contact map calculation to given residue range | |
| + | ; -read file : read reference contact list from file | ||
| + | ; -list : write out contact list | ||
== Examples == | == Examples == | ||
Latest revision as of 02:28, 28 July 2009
Usage
usage: contact.pl [options] [refPDB] cmpPDB
options: [-l min:max[...]]
[-read file]
[-list]
[-mindist value]
[-betweenchains]
Description
This script calculates residue contact maps and compares them between
different structures. Residues are considered in contact when the minimum
inter-residue distance of all pairs of heavy atoms is less than
4.2 Å.
In the default mode with two structures as arguments the fraction of contacts
present in the second structure with respect to the first is determined.
Also calculated is the continuous quantity rho that uses a sigmoidal function
for the minimum inter-residue distance around 4.2 A to effectively include
residue pairs that are slightly further apart with a reduced weight.
An extended output is available with -list to get a list of all residue
contacts in the reference structure with the minimum distances in the reference
as well as the test structures.
If only one structure is given as an argument no comparison is done. A residue
contact list is printed out instead. This list can be used in later comparisons
with -read to save time if multiple structures are compared to the same
reference. The more costly calculation of the reference residue map then
has to be done only once.
The option -l is available to limit the residue map to contacts with a subset of residues as might be useful for loop modeling.
Options
- -help
- usage information
- -l min:max[...]
- restrict contact map calculation to given residue range
- -read file
- read reference contact list from file
- -list
- write out contact list
Examples
contact.pl 1vii.exp.pdb 1vii.exp.min.pdb
compares the residue contact map between two structures and reports
the number of contacts present in the second structure with
respect to the first. Also reported is the continuous quantity rho
that takes near-contacts into consideration.
23 contacts ( fraction: 0.958333 ), rho: 0.999182
contact.pl 1vii.exp.pdb
writes the contact list for the given structure to standard output
2 7 3.525115 2 10 3.383307 2 11 3.541492 2 15 2.839893 2 34 2.930046 2 36 3.797043 7 12 3.996071 7 13 2.808753 7 14 2.851043 7 15 2.858498 ...
contact.pl -read 1vii.exp.contacts 1vii.exp.min.pdb
compares the residue contact map of the given structure with
the contact list read from a file and reports
the number of contacts present with respect to the reference.
Also reported is the continuous quantity rho
that takes near-contacts into consideration.
23 contacts ( fraction: 0.958333 ), rho: 0.999182
contact.pl -l 10:21 -list 1vii.exp.pdb 1vii.exp.min.pdb
compares the residue contact map involving only contacts with residues 10
through 21 between two structures. In addition to the fraction of
contacts present in the second structure a detailed list is printed
out for all contacts with the minimum distances in the reference and
test structures.
19 contacts ( fraction: 0.950000 ), rho: 0.999018 LEU:2 - VAL:10 3.383307 4.250682 * LEU:2 - PHE:11 3.541492 3.911385 * LEU:2 - ARG:15 2.839893 2.706345 * PHE:7 - GLY:12 3.996071 2.764539 * PHE:7 - MET:13 2.808753 3.330530 * PHE:7 - THR:14 2.851043 3.908893 * PHE:7 - ARG:15 2.858498 3.255971 * PHE:7 - PHE:18 3.632217 3.699490 * VAL:10 - LYS:33 3.377613 2.759139 ...