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 without extension: one.split(".",1)[0]
cmd.load(one, name1)
cmd.load(two, name2)
rms = cmd.align(name1, name2)
print(rms)
cmd.quit()
On Tue, Jul 14, 2015 at 2:02 AM, Gazal <gazal...@gmail.com> wrote:
> 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 space groups.
>
> And I think it works now...
>
> I get following RMSD value:
> (1.246872901916504, 581, 5, 2.418435573577881, 669, 94.0, 113)
>
> these values are:
> RMSD
> No. of atoms for which we get RMSD
> No. of cycles
> ??
> No. of atoms aligned
> ??
> ??
>
> :)
>
> But still there is this space group problem.. Any suggestions to beat that?
>
>
>
> Many thanks.
>
> --
> Gazal
>
> On Sat, Jul 11, 2015 at 10:17 PM, David Hall <li...@cowsandmilk.net>
> wrote:
>
>> 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 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
>> 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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