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
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 h
On Tue, 2014-01-07 12:05 EST, Jed Goldstone 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 only wants to ali
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"))
Che
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 wrote:
> If the Wild-Type is called wild
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 informa
