[Chimera-users] Writing each rotamers to individual PDB file

Chemmama, Ilan Ilan.Chemmama at ucsf.edu
Wed Feb 17 15:42:22 PST 2021

Hi Eric,

Thank you for the reply.
I have a couple of follow up questions if I may.

(i) I have run the script you attached but I get a few errors:

rots=get_rotamers(res, resType=rot_type)

gives only two rotamers (`len(rots))`. When I run this on the GUI, I get 54 rotamers which is what I would expect.

(ii) I get a Chimera error:
File "/opt/chimera-1.14-1.fc31/share/chimera/triggerSet.py", line 83, in invoke
    self._funcData, triggerData)
  File "/opt/chimera-1.14-1.fc31/share/chimera/Sequence.py", line 401, in wrapper2
    s._residueCB(a1, a2, a3)
  File "/opt/chimera-1.14-1.fc31/share/chimera/Sequence.py", line 626, in _residueCB
    if res3to1(res.type) != ungapped[pos]:
IndexError: string index out of range

Error processing trigger "Residue":
IndexError: string index out of range

  File "/opt/chimera-1.14-1.fc31/share/chimera/Sequence.py", line 626, in _residueCB
    if res3to1(res.type) != ungapped[pos]:

I found a workaround in the mean time.
I managed to make Chimera saved all the rotamers in a single PDB file, and an extra character was added to RES_NAME entry in the PDB file to differentiate each rotamer.
Then I just did some file manipulations and split the PDB appropriately.

Thanks again !

On Feb 17, 2021, at 2:40 PM, Eric Pettersen <pett at cgl.ucsf.edu<mailto:pett at cgl.ucsf.edu>> wrote:

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: https://urldefense.proofpoint.com/v2/url?u=http-3A__dunbrack.fccc.edu_bbdep2010_&d=DwIFAg&c=iORugZls2LlYyCAZRB3XLg&r=mKSDZidXHAmavIl-Ov-liBnCRR7Q81s96Ue3o_9uiv0&m=WhkU7bXdiTiHIgdIWawwnAeUYVvhC0LnZfTGG8GEpVY&s=S3jcExeF5rf7cB2J3ns5Mwa8Btp-FXWolMsa3v2ysno&e=  .  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 Pettersen
UCSF Computer Graphics Lab

On Feb 16, 2021, at 7:24 PM, Chemmama, Ilan <Ilan.Chemmama at ucsf.edu<mailto: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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