contact.pl - Revision history

Edit: /* Options */

2009-07-28T02:28:15Z

Options

Edit: /* Description */

2009-07-28T02:27:09Z

Description

Feig at 15:49, 8 August 2008

2008-08-08T15:49:54Z

210.19.71.60: /* Usage */

2008-08-06T13:39:19Z

Usage

Feig at 14:07, 12 August 2006

2006-08-12T14:07:10Z

New page

__NOTOC__
== 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. 
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

== 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>

←Older revision		Revision as of 13:39, 6 August 2008
Line 1:		Line 1:
−	~~__NOTOC__~~	+	dummy
−	~~== 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>~~

@@ Line 34: / Line 34: @@
 ; -help : usage information
+; -l min&#58;max[...] : restrict contact map calculation to given residue range
 == Examples ==

@@ Line 9: / Line 9: @@
 different structures. Residues are considered in contact when the minimum
 inter-residue distance of all pairs of heavy atoms is less than
-.2A.<BR>
+.2 &Aring;.<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.
@@ Line 19: / Line 20: @@
 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
@@ Line 25: / Line 27: @@
 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.

←Older revision		Revision as of 15:49, 8 August 2008
Line 1:		Line 1:
−	~~dummy~~	+	__NOTOC__
		+	== 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>