MMTSB
Tool Set Documentation

Difference between revisions of "contact.pl"

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== Usage ==
 
 
 
<mmtsbToolUsage cmd="contact.pl"></mmtsbToolUsage>
 
 
 
== 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
 
4.2A.<BR>
 
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 <B>-list</B> 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.
 
<BR>
 
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 <B>-read</B> 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.
 
<BR>
 
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.
 
 
 
== Options ==
 
 
 
; -help : usage information
 
 
 
 
 
== Examples ==
 
 
 
<mmtsbToolExample cmd="contact.pl" set="/apps/mmtsb/bench/contact.pl-test/test1"></mmtsbToolExample>
 
 
 
<mmtsbToolExample cmd="contact.pl" set="/apps/mmtsb/bench/contact.pl-test/test2"></mmtsbToolExample>
 
 
 
<mmtsbToolExample cmd="contact.pl" set="/apps/mmtsb/bench/contact.pl-test/test3"></mmtsbToolExample>
 
 
 
<mmtsbToolExample cmd="contact.pl" set="/apps/mmtsb/bench/contact.pl-test/test4"></mmtsbToolExample>
 

Revision as of 13:39, 6 August 2008

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