I assume you are referring to
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/fitting.py
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/fitting.py
That is a script that creates a function. To turn it into a program, you need
to set up what you read in and what you output.
In python, this is often done by command line arguments that can read from
sys.argv
import sys
arg1 = sys.argv[1]
arg2 = sys.argv[2]
cmd.load(arg1, “protein1”)
cmd.load(arg2, “protein2”)
You can have the definition of fitting in your script, then call
fitting(“protein1”, , “protein2”, )
I left in questions for the select1 and select2 arguments of the function since
it is not at all clear what you would like to put in as arguments there.
Beyond that, I would recommend reading up on python assuming you are not
familiar with the language.
-David
On Jul 11, 2015, at 10:00 AM, Gazal gazal...@gmail.com wrote:
Thank you for your help, Osvaldo and David.
I tried using the command but did not get the RMS as expected.. Following are
the results:
1.
pymol -cqr fitting.py 1A6M.pdb 4OE9.txt
PyMOLrun fitting.py,main
HEADEROXYGEN TRANSPORT26-FEB-98 1A6M
TITLE OXY-MYOGLOBIN, ATOMIC RESOLUTION
COMPNDMOL_ID: 1;
COMPND 2 MOLECULE: MYOGLOBIN;
COMPND 3 CHAIN: A
ObjectMolecule: Read secondary structure assignments.
ObjectMolecule: Read crystal symmetry information.
Symmetry: Found 2 symmetry operators.
CmdLoad: 1A6M.pdb loaded as 1A6M.
HEADERPROTEIN BINDING 12-JAN-14 4OE9
TITLE THE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF COMMD9
COMPNDMOL_ID: 1;
COMPND 2 MOLECULE: COMM DOMAIN-CONTAINING PROTEIN 9;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: COMMD9, UNP RESIDUES 1-117;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES
ObjectMolecule: Read secondary structure assignments.
ObjectMolecule: Read crystal symmetry information.
Symmetry: Found 1 symmetry operators.
CmdLoad: 4OE9.txt loaded as 4OE9.txt.
2.
pymol -cqr fitting.py --1A6M.pdb 4OE9.txt
PyMOLrun fitting.py,main
Do I need to import Pymol module in the shell script to use the pymol scripts
like you did in python?
Am I missing something?
Thanks
--
Gazal
On Fri, Jul 10, 2015 at 11:36 PM, David Hall li...@cowsandmilk.net
mailto:li...@cowsandmilk.net wrote:
http://www.pymolwiki.org/index.php/Command_Line_Options
http://www.pymolwiki.org/index.php/Command_Line_Options
see the -c and -r options. I also use -q
pymol -qcr script.py — arg1 arg2 arg3
On Jul 10, 2015, at 8:44 AM, Gazal gazal...@gmail.com
mailto:gazal...@gmail.com wrote:
Hi,
I'm trying to find the RMSD values for batch purposes. The command which I
found works for the Pymol-command line.
I was hoping if I could get an idea about using the python script fitting.py
in my shell script without triggering the Pymol GUI.
Thanks in advance.
Gazal
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