Ccp4 pisa

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Type Python Script
Download ccp4_pisa.py
Author(s) Gerhard Reitmayr and Dalia Daujotyte
License GPL
This code has been put under version control in the project Pymol-script-repo

Overview

The script selects atoms from the list of the contacts found by PISA. First, we run PISA on our pdb file to find the interfaces. Then by using the ccp4_pisa script in PyMOL we separately select atoms for all interface types and individual interfaces. This generates many selections, two for each interface, allowing quick manipulation of (sometimes) extensive lists in PISA log file.

Usage

ccp4_pisa( pisafile )


Example 1

The script parses the XML output files from the PISA service or command line tool. A short description of how to download the XML output files is available here http://www.ebi.ac.uk/msd-srv/prot_int/pi_download.html.

(For example, the following URL downloads the interfaces in 2c7r.pdb http://www.ebi.ac.uk/pdbe/pisa/cgi-bin/interfaces.pisa?2c7r)

Make sure you import the ccp4_pisa script first.

Download: examples/ccp4_pisa_1.pml
This code has been put under version control in the project Pymol-script-repo
reinitialize
import ccp4_pisa
 
fetch 2c7r, async=0
preset.pretty("2c7r")
 
python
if 'PYMOL_GIT_MOD' in os.environ:
    example_dir = os.path.join(os.path.split(os.environ['PYMOL_GIT_MOD'])[0],"files_for_examples")
    pisafile = os.path.join(example_dir,"2c7r.pisa")
else:
    pisafile = "2c7r.pisa"
python end
 
ccp4_pisa.ccp4_pisa(pisafile)
 
python
for selname in cmd.get_names('selections')[1:]:
    cmd.create("O_%s"%selname,selname)
    cmd.show("spheres","O_%s"%selname)
    cmd.disable("O_%s"%selname)
    cmd.group("Selections",selname)
    cmd.group("Objects","O_%s"%selname)
python end
 
 
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