View source for Ccp4 ncont

{{Infobox script-repo
|type      = script
|filename  = scripts/ccp4_ncont.py
|author    = [[User:Dalyte|Gerhard Reitmayr and Dalia Daujotyte]]
|license   = GPL
}}

== Overview ==
[[File:HhaExample.png|thumb|300px|right|Interface residues (at cutoff <4A) in the 2c7r.pdb were found using NCONT. Usage of ccp4_ncont script in PyMOL allows easy selection of residues and atoms listed in ncont.log file. Interacting protein and DNA residues are colored in red and slate, respectively. Atoms in contact are shown in dots.]]

The script selects residues and atoms from the list of the contacts found by NCONT from CCP4 Program Suite (NCONT analyses contacts between subsets of atoms in a PDB file).
First, we run NCONT on our pdb file to find interface residues. Then by using the ccp4_ncont script in PyMOL we separately select residues and atoms listed in a ncont.log file. This generates two selections (atoms and residues) for each interacting chain, allowing quick manipulation of (sometimes) extensive lists in NCONT log file.

This script works best for intermolecular contacts (when NCONT target and source selections don't overlap). If crystal contacts (NCONT parameter cell = 1 or 2) are included then additional coding is required to distinguish inter from intramolecular contacts.
     
== Usage ==

ccp4_ncont( contactsfile, selName1 = "source", selName2 = "target" )


== Examples ==


First use NCONT to find interface residues/atoms in the pdb file. Once you have ncont.log file proceed to PyMOL.
Make sure you import the ccp4_ncont script first.
 
 fetch 2c7r
 ccp4_ncont 2c7r.ncont, selName1=prot, selName2=dna

[[File:HhaI20example.png|thumb|300px|right|Quick and easy selection of interacting residues and atoms listed in the NCONT log file. Protein and DNA residues are colored in red and slate, respectively. Atoms in contact are shown in dots.]]

{{Template:PymolScriptRepoDownload|examples/ccp4_ncont_1.pml}}
<include src="https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/examples/ccp4_ncont_1.pml" highlight="python" />

== Getting a NCONT file ==

=== Install CCP4 - for Linux ===
Goto: http://www.ccp4.ac.uk/download.php <br>
Click: automated Downloads Pages <br>
Select: Linux, generic linux (x86) <br>
Select: Customized installation <br>
Select: Only CCP4 Program Suite, Executables -> Continue <br>
No additional packages -> Continue <br>
Download <br>

Extract for example to: '''/home/YOU/Software/CCP'''4 <br>
Then run: <br>
<syntaxhighlight lang="bash">
$ /home/YOU/Software/CCP4/install.sh
</syntaxhighlight>
write yes, read agreement, push y to agree license <br> 
For sourcing scripts, say yes. <br>
See the changes to your environmental virables: <br>
<syntaxhighlight lang="bash">
$ less ~/.bashrc
</syntaxhighlight>

=== Use of NCONT - for Linux ===
See here for the NCONT program and options: <br>
http://www.ccp4.ac.uk/html/ncont.html <br>
http://www.ccp4.ac.uk/html/pdbcur.html#atom_selection <br>
Locate the pdb, and now run in terminal: <br>
<syntaxhighlight lang="bash">
$ ncont XYZIN 2c7r.pdb >> 2c7r.ncont << eof   (#press enter)
> source A    (#press enter)
> target C,D  (#press enter)
> eof         (#press enter, and now the program runs, and shell saves to 2c7r.ncont)
</syntaxhighlight>


[[Category:Script_Library]]
[[Category:ThirdParty Scripts]]
[[Category:Structural Biology Scripts]]
[[Category:Pymol-script-repo]]