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
PyMOL>run fitting.py,main
HEADER OXYGEN TRANSPORT 26-FEB-98 1A6M
TITLE OXY-MYOGLOBIN, ATOMIC RESOLUTION
COMPND MOL_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".
HEADER PROTEIN BINDING 12-JAN-14 4OE9
TITLE THE CRYSTAL STRUCTURE OF THE N-TERMINAL DOMAIN OF COMMD9
COMPND MOL_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
PyMOL>run 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> wrote:
> 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> 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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