Hi Ilan, 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()[0] 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. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Feb 16, 2021, at 7:24 PM, Chemmama, Ilan <Ilan.Chemmama@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 ! Ilan _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users