Ccp4 pisa: Difference between revisions
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|type = script | |type = script | ||
|filename = ccp4_pisa.py | |filename = ccp4_pisa.py | ||
|author = [[ | |author = [[User:Dalyte|Gerhard Reitmayr and Dalia Daujotyte]] | ||
|license = GPL | |license = GPL | ||
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[[Category:Script_Library]] [[Category:ThirdParty Scripts]] [[Category:Structural Biology Scripts]] | [[Category:Script_Library]] | ||
[[Category:ThirdParty Scripts]] | |||
[[Category:Structural Biology Scripts]] | |||
[[Category:Pymol-script-repo]] | |||
Latest revision as of 17:17, 13 February 2012
| 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 | |
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