Re: [PyMOL] How to find RMSD values using fitting.py using Shell script

Thanks. Heres how I did it: import __main__ __main__.pymol_argv = ['pymol', '-qc'] import pymol import os from pymol import * pymol.finish_launching() one= '/protein_files/1A6M.pdb' two = '/protein_files/1GZX.pdb' name1 = os.path.basename(one) name2 = os.path.basename(two) # To get filename wit

Re: [PyMOL] How to find RMSD values using fitting.py using Shell script

Thanks, I tried using python like you suggested but received these errors: Symmetry-Error: Urecognized space group symbol 'P 21 21 2 A'. Symmetry-Error: Unable to get matrices. I used the method given by Osvaldo. And to test if it works I removed the lines from pdb files where it mentioned the sp

Re: [PyMOL] How to find RMSD values using fitting.py using Shell script

I assume you are referring to 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 pytho

Re: [PyMOL] How to find RMSD values using fitting.py using Shell script

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 HEADEROXYGEN TRANSPORT26-FEB-98 1A6M TITLE OXY-MYOGLOBIN, A

Re: [PyMOL] How to find RMSD values using fitting.py using Shell script

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 wrote: > > Hi, > > I'm trying to find the RMSD values for bat

Re: [PyMOL] How to find RMSD values using fitting.py using Shell script

Hi Gazal, Generally when I want to do batch operations using PyMOL I wrote a Python script and I call PyMOL from within that script. I prefer this way because I think is more flexible and simple than using PyMOL from the command line. In those cases I start the Python script with the following imp

[PyMOL] How to find RMSD values using fitting.py using Shell script

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 --