[Chimera-users] Writing each rotamers to individual PDB file
pett at cgl.ucsf.edu
Wed Feb 17 14:40:14 PST 2021
I see that the Dunbrack 2010 rotamer library is now being released under a more permissive license than previously, so this kind of quasi-bulk dumping of library info is probably okay. Nonetheless, since you are using the library so extensively it would be nice of you to register as a library user here if you could: http://dunbrack.fccc.edu/bbdep2010/ . And of course if any publication results from it, cite the paper shown in the Rotamers dialog.
Okay, that said, you are going to have to use a Python script to do what you want. Assuming you have somehow selected the residue involved, to get all rotamers of LYS for it, the heart of the script would be:
from chimera import runCommand as run
from Rotamers import getRotamers
from chimera import selection
rot_type = "LYS"
res = selection.currentResidues()
rots = getRotamers(res, resType=rot_type)
for i in range(len(rots)):
run("swapaa %s sel criteria %d" % (rot_type, i+1))
run("write 0 /path/to/save/folder/struct%s%d.%d.pdb" % (rot_type, res.id.position, i+1))
Let me know If you need more help than that.
UCSF Computer Graphics Lab
> On Feb 16, 2021, at 7:24 PM, Chemmama, Ilan <Ilan.Chemmama at ucsf.edu> wrote:
> Dear Developers,
> I am trying to write a PDB for each rotamer in Chimera.
> I run the command:
> `swapaa RES :RESNUM lib Dunbrack criteria manual`
> I get the enumeration for each rotamers from SCRWL library.
> I was wondering if there was a way to write each of those rotamers into separate PDB file using a script.
> Some residues have large number of possible rotamers and manually selecting the rotamer and saving the PDB file is not tractable.
> Thank you very much !
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