Hi Om -
Here is another option that loads only one mutant at a time. You can save the
following as a Python script (e.g., "mut-rmsd.py") and run it from the PyMOL
command line by typing `run mut-rmsd.py` (with a full or relative path if it's
not in PyMOL's working directory).
For more information about these functions, you can also check out a few things
on the PyMOL Wiki:
http://pymolwiki.org/index.php/Process_All_Files_In_Directory
http://pymolwiki.org/index.php/Align
### begin script ###
from pymol import cmd
from glob import glob
# Edit these two variables with the paths to your files
wt_file = "wt.pdb"
mut_glob = "mut/*.pdb"
# load the wild-type pdb
cmd.load(wt_file,"wt")
# loop through the mutants
for file in glob(mut_glob):
print file
cmd.load(file,"mut")
rms = cmd.align("wt","mut")[0]
print " %s rmsd: %s" % (file,rms)
cmd.delete("mut")
### end script ###
Hope that helps.
Cheers,
Jared
--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Avenue
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/
On Jan 7, 2014, at 11:58 AM, Om Shiv
<harhaalmekhu...@gmail.com<mailto:harhaalmekhu...@gmail.com>> wrote:
Hello All
I am a new user to Pymol and Python.
I have a PDB Structure with single chain (A) and I have modeled 500 single
point mutants of this wild structure.
Now for each such 500 modeled structures, I would like to calculate RMSD (ALL
ATOMS) with the wild type PDB structure.
Can anybody help me with the script to automate calculation of 500 RMSD
calculations using PYMOL ?
Secondly, what threshold value of RMSD can be considered above which we can say
that the mutant structure is considerably different than the wild type ?
Thanks in advance.
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