Hello
I am using the following script file:
### 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 =
Hi Om,
asides from the usual list of suspects like access permissions try double
backslashes or a raw string in your path-filenames. Python on Windows is a bit
peculiar in that respect. Read up on raw strings in the Python docs.
Try
wt_file =
Thanks, Carsten. I thought it would turn out to be something related to the
paths, but couldn't put my finger on it.
(I was able to run the script fine without either of those fixes on Incentive
PyMOL 1.5.0 32-bit on a Win XP VirtualBox VM guest on a Mac OS 10.8 host. Not
sure why that might
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.
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
Check out Robert Campbell's Pymol script repository.
I think align_all_to_all.py should do what you want, including exporting
RMSD values.
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
Jed
On 1/7/2014 11:58 AM, Om Shiv wrote:
Hello All
I am a new user to Pymol and Python.
I have
On Tue, 2014-01-07 12:05 EST, Jed Goldstone jgoldst...@whoi.edu wrote:
Check out Robert Campbell's Pymol script repository.
I think align_all_to_all.py should do what you want, including exporting
RMSD values.
http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
Actually, I think Om
If the Wild-Type is called wildtype:
rmsds = [(i,cmd.align(i,wildtype)[0]) for i in cmd.get_object_list(not
wildtype)]
print rmsds
or, writing out the results directly
open(rmsds.dat,w).writelines(%s %f\n%(i,cmd.align(i,wildtype)[0])
for i in cmd.get_object_list(not wildtype))
Cheers,
Tsjerk
I like to add that to get the ALL ATOMS RMSD you need to pass cycles=0 to
cmd.align or to Rob's align_allfiles. Otherwise, the outlier rejection
refinement might drop atoms from the alignment.
Cheers,
Thomas
On 07 Jan 2014, at 13:58, Tsjerk Wassenaar tsje...@gmail.com wrote:
If the
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
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