On Feb 17, 2021, at 3:42 PM, Chemmama, Ilan <Ilan.Chemmama@ucsf.edu> wrote:

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:

rot_type=“GLU"

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 ! 

Ilan

On Feb 17, 2021, at 2:40 PM, Eric Pettersen <pett@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

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
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