Re: [PyMOL] How to automate RMSD calculation for large no of structures

[Sampson, J. <Jar...@ny...>]

Hi Om -

I hope you don't mind me posting your questions back to the list.  (When replying to this list, you have to use Reply All, otherwise it just goes to the sender.)

Also, a quick disclaimer: I haven't used PyMOL on Windows in over 5 years, so what I'm saying may not be entirely accurate.  (Others, please correct me if there's anything incorrect here.)


Hi I have installed Pymol in windows 7 platform. Why does it not allow me to save the script in the Pymol folder ?

 Is there any way to save it in Pymol working directory ?

I don't think you really want to save it to the folder where PyMOL is installed (if that's what you mean by "the Pymol folder").  The working directory is the directory from which PyMOL is launched.  You can see where this is by typing `pwd` at the PyMOL command prompt.  Some other shell commands work as well, such as `cd` and `ls`.


Thanks for your guidance.

I have modified your script as follows:

### begin script ###

from pymol import cmd
from glob import glob

# Edit these two variables with the paths to your files
wt_file = "D:\STUDY\STRUCTURE_PPT\RMSD\Pymol\Original\1APS.pdb"
mut_glob = "D:\STUDY\STRUCTURE_PPT\RMSD\Pymol\models\1APS\1APS_*.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 ###

Used the following command from the command line:  run D:\STUDY\STRUCTURE_PPT\RMSD\mut-rmsd.py

But I am receiving the following error:

IOError: [Errno 2] No such file or directory: 'D:\\STUDY\\STRUCTURE_PPT\\RMSD\\mut-rmsd.py'<smb://STUDY//STRUCTURE_PPT//RMSD//mut-rmsd.py'>

Please help.
thanks

Maybe try using the GUI:

1. File > Log... - create a log file (I usually call mine "log.pml"), which will be useful later.
2. File > Run... - navigate to your mut-rmsd.py file and run it.
3. Go back and open your log file to see what the command looked like when you ran the script.

PyMOL log files are very widely useful for finding out how to translate GUI actions into scriptable commands.

Hope that helps!

Cheers,
Jared



On Wed, Jan 8, 2014 at 1:13 AM, Sampson, Jared <Jar...@ny...<mailto:Jar...@ny...>> wrote:
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 <har...@gm...<mailto:har...@gm...>> 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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