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 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
>
> On Tue, Jan 7, 2014 at 7:20 PM, Robert Campbell <robert.campb...@queensu.ca>
> wrote:
> 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 only wants to align the individual mutants to the
> wild-type not all 500 mutants against each other which is what the above
> script does. Also, I think for 500 structure you probably don't want to
> load all 500 in at one time, so it would be better to have a script that
> only loads each mutant one at a time, calculates its RMSD to the wild-type
> and then deletes it.
>
> I have modified my align_all.py script to create a new one called
> align_allfiles.py and added that to the above website. It is also attached
> here. To specify the use of all atoms simply add that to the mobile and
> target selections. You can also specify PyMOL's cutoff and cycles
> arguments to the align function (defaults to cycles=5, cutoff=2)
>
> align_allfiles target_model, files=mutants*.pdb, mobile_selection=all,
> target_selection=all
>
> It will print out a list of RMSD values for each mutant in order read in as
> well as sorted by RMSD.
>
>
> Cheers,
> Rob
>
> > Jed
> >
> >
> > On 1/7/2014 11:58 AM, Om Shiv 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.
> > >
>
> --
> Robert L. Campbell, Ph.D.
> Senior Research Associate/Adjunct Assistant Professor
> Dept. of Biomedical & Molecular Sciences
> Botterell Hall Rm 644
> Queen's University,
> Kingston, ON K7L 3N6 Canada
> Tel: 613-533-6821
> <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc
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