swapaa: choosing rotamers
Dear all, I would like to use swapaa and choose which rotamer I want. Foe example I want from library dynameomics the second rotamer that appears in the pop-up menu of Arg. is it possible? Thank you for your time, Alex
Dear Alex, Not directly, the “swapaa” command only uses the ranking rules that you tell it to use. Only if the rules happened to choose that rotamer would you get it. To directly choose a specific rotamer as listed in the rotamers dialog, you would have to use that dialog (Rotamers graphical user interface). The rules are specified with the “criteria” option of swapaa, see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html#criteria> Rotamers graphical interface: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html> Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jul 1, 2015, at 4:57 AM, roz orchidea <roz.orchidea@gmail.com> wrote:
Dear all, I would like to use swapaa and choose which rotamer I want. Foe example I want from library dynameomics the second rotamer that appears in the pop-up menu of Arg. is it possible? Thank you for your time, Alex
Hi Alex, To get specifically get the second most probable rotamer you add the "criteria" keyword to the swapaa command with the value "2", e.g.: swapaa ASP :41.a criteria 2 You don't really say why you specifically want the second rotamer. Are you trying out all the rotamers one by one? You might want to consider doing that via the a Python script that uses the functions in the Rotamers module. That way you can find out how many rotamers are available, which isn't really possible with just the swapaa command. Another thing to consider is that if you know the chi angles you want, you can just swap to the new residue type and then request those specific chi values. For example to change residue 41.A to ASP and set its chis to 40 and 75: swapaa ASP :41.a setattr a chi1 40 :41.a setattr a chi2 75 :41.a --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Jul 1, 2015, at 9:32 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Alex, Not directly, the “swapaa” command only uses the ranking rules that you tell it to use. Only if the rules happened to choose that rotamer would you get it. To directly choose a specific rotamer as listed in the rotamers dialog, you would have to use that dialog (Rotamers graphical user interface).
The rules are specified with the “criteria” option of swapaa, see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html#criteria>
Rotamers graphical interface: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 1, 2015, at 4:57 AM, roz orchidea <roz.orchidea@gmail.com> wrote:
Dear all, I would like to use swapaa and choose which rotamer I want. Foe example I want from library dynameomics the second rotamer that appears in the pop-up menu of Arg. is it possible? Thank you for your time, Alex
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Also, the "lib" keyword to the swapaa command allows you to pick the library to use, e.g.: swapaa ASP :41.a lib dynameomics criteria 2 --Eric On Jul 1, 2015, at 10:01 AM, Eric Pettersen <pett@cgl.ucsf.EDU> wrote:
Hi Alex, To get specifically get the second most probable rotamer you add the "criteria" keyword to the swapaa command with the value "2", e.g.: swapaa ASP :41.a criteria 2 You don't really say why you specifically want the second rotamer. Are you trying out all the rotamers one by one? You might want to consider doing that via the a Python script that uses the functions in the Rotamers module. That way you can find out how many rotamers are available, which isn't really possible with just the swapaa command. Another thing to consider is that if you know the chi angles you want, you can just swap to the new residue type and then request those specific chi values. For example to change residue 41.A to ASP and set its chis to 40 and 75:
swapaa ASP :41.a setattr a chi1 40 :41.a setattr a chi2 75 :41.a
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jul 1, 2015, at 9:32 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Alex, Not directly, the “swapaa” command only uses the ranking rules that you tell it to use. Only if the rules happened to choose that rotamer would you get it. To directly choose a specific rotamer as listed in the rotamers dialog, you would have to use that dialog (Rotamers graphical user interface).
The rules are specified with the “criteria” option of swapaa, see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html#criteria>
Rotamers graphical interface: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 1, 2015, at 4:57 AM, roz orchidea <roz.orchidea@gmail.com> wrote:
Dear all, I would like to use swapaa and choose which rotamer I want. Foe example I want from library dynameomics the second rotamer that appears in the pop-up menu of Arg. is it possible? Thank you for your time, Alex
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Thank you both for your answers! Eric I am not trying all rotamers, I just want to have some specific rotamers in the binding sites of my protein-DNA models. I am using a python script to call chimera and a cmd script with all the swapaa commands that I need. Is there another way? Thank you for your time, Alex 2015-07-01 19:03 GMT+02:00 Eric Pettersen <pett@cgl.ucsf.edu>:
Also, the "lib" keyword to the swapaa command allows you to pick the library to use, e.g.: swapaa ASP :41.a lib dynameomics criteria 2
--Eric
On Jul 1, 2015, at 10:01 AM, Eric Pettersen <pett@cgl.ucsf.EDU> wrote:
Hi Alex, To get specifically get the second most probable rotamer you add the "criteria" keyword to the swapaa command with the value "2", e.g.: swapaa ASP :41.a criteria 2 You don't really say why you specifically want the second rotamer. Are you trying out all the rotamers one by one? You might want to consider doing that via the a Python script that uses the functions in the Rotamers module. That way you can find out how many rotamers are available, which isn't really possible with just the swapaa command. Another thing to consider is that if you know the chi angles you want, you can just swap to the new residue type and then request those specific chi values. For example to change residue 41.A to ASP and set its chis to 40 and 75:
swapaa ASP :41.a setattr a chi1 40 :41.a setattr a chi2 75 :41.a
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jul 1, 2015, at 9:32 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Alex, Not directly, the “swapaa” command only uses the ranking rules that you tell it to use. Only if the rules happened to choose that rotamer would you get it. To directly choose a specific rotamer as listed in the rotamers dialog, you would have to use that dialog (Rotamers graphical user interface).
The rules are specified with the “criteria” option of swapaa, see: < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html#criteria
Rotamers graphical interface: <
http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot....
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 1, 2015, at 4:57 AM, roz orchidea <roz.orchidea@gmail.com>
wrote:
Dear all, I would like to use swapaa and choose which rotamer I want. Foe
example I want from library dynameomics the second rotamer that appears in the pop-up menu of Arg. is it possible?
Thank you for your time, Alex
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Dear Alex, Instead of calling chimera from a python script, you can simply use chimera's python to run the script and call the command line commands with the runCommand() function. This way, you can have just the python script and avoid the cmd dependency. You can run the following script with "chimera --nogui script.py": """ import chimera from chimera import runCommand as rc rc('open 1BPT') rc('swapaa tyr :5; swapaa phe :7') """ Best, Matej --------------------------------- Dr. Matej Repic Ecole Polytechnique Fédérale de Lausanne Laboratory of Computational Chemistry and Biochemistry SB - ISIC – LCBC BCH 4108 CH - 1015 Lausanne ------------------------------------------------------ From: <chimera-users-bounces@cgl.ucsf.edu<mailto:chimera-users-bounces@cgl.ucsf.edu>> on behalf of roz orchidea <roz.orchidea@gmail.com<mailto:roz.orchidea@gmail.com>> Date: Thursday, July 9, 2015 at 12:49 To: "chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>" <chimera-users@cgl.ucsf.edu<mailto:chimera-users@cgl.ucsf.edu>> Subject: Re: [Chimera-users] swapaa: choosing rotamers Thank you both for your answers! Eric I am not trying all rotamers, I just want to have some specific rotamers in the binding sites of my protein-DNA models. I am using a python script to call chimera and a cmd script with all the swapaa commands that I need. Is there another way? Thank you for your time, Alex 2015-07-01 19:03 GMT+02:00 Eric Pettersen <pett@cgl.ucsf.edu<mailto:pett@cgl.ucsf.edu>>: Also, the "lib" keyword to the swapaa command allows you to pick the library to use, e.g.: swapaa ASP :41.a lib dynameomics criteria 2 --Eric On Jul 1, 2015, at 10:01 AM, Eric Pettersen <pett@cgl.ucsf.EDU<mailto:pett@cgl.ucsf.EDU>> wrote:
Hi Alex, To get specifically get the second most probable rotamer you add the "criteria" keyword to the swapaa command with the value "2", e.g.: swapaa ASP :41.a criteria 2 You don't really say why you specifically want the second rotamer. Are you trying out all the rotamers one by one? You might want to consider doing that via the a Python script that uses the functions in the Rotamers module. That way you can find out how many rotamers are available, which isn't really possible with just the swapaa command. Another thing to consider is that if you know the chi angles you want, you can just swap to the new residue type and then request those specific chi values. For example to change residue 41.A to ASP and set its chis to 40 and 75:
swapaa ASP :41.a setattr a chi1 40 :41.a setattr a chi2 75 :41.a
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jul 1, 2015, at 9:32 AM, Elaine Meng <meng@cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote:
Dear Alex, Not directly, the “swapaa” command only uses the ranking rules that you tell it to use. Only if the rules happened to choose that rotamer would you get it. To directly choose a specific rotamer as listed in the rotamers dialog, you would have to use that dialog (Rotamers graphical user interface).
The rules are specified with the “criteria” option of swapaa, see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html#criteria>
Rotamers graphical interface: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot.html>
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 1, 2015, at 4:57 AM, roz orchidea <roz.orchidea@gmail.com<mailto:roz.orchidea@gmail.com>> wrote:
Dear all, I would like to use swapaa and choose which rotamer I want. Foe example I want from library dynameomics the second rotamer that appears in the pop-up menu of Arg. is it possible? Thank you for your time, Alex
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
I will try it! Thanks a lot! 2015-07-09 14:43 GMT+02:00 Repic Matej <matej.repic@epfl.ch>:
Dear Alex,
Instead of calling chimera from a python script, you can simply use chimera's python to run the script and call the command line commands with the runCommand() function. This way, you can have just the python script and avoid the cmd dependency.
You can run the following script with "chimera --nogui script.py":
""" import chimera from chimera import runCommand as rc rc('open 1BPT') rc('swapaa tyr :5; swapaa phe :7') """
Best, Matej
--------------------------------- Dr. Matej Repic Ecole Polytechnique Fédérale de Lausanne Laboratory of Computational Chemistry and Biochemistry SB - ISIC – LCBC BCH 4108 CH - 1015 Lausanne ------------------------------------------------------
From: <chimera-users-bounces@cgl.ucsf.edu> on behalf of roz orchidea < roz.orchidea@gmail.com> Date: Thursday, July 9, 2015 at 12:49 To: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] swapaa: choosing rotamers
Thank you both for your answers! Eric I am not trying all rotamers, I just want to have some specific rotamers in the binding sites of my protein-DNA models. I am using a python script to call chimera and a cmd script with all the swapaa commands that I need. Is there another way?
Thank you for your time, Alex
2015-07-01 19:03 GMT+02:00 Eric Pettersen <pett@cgl.ucsf.edu>:
Also, the "lib" keyword to the swapaa command allows you to pick the library to use, e.g.: swapaa ASP :41.a lib dynameomics criteria 2
--Eric
On Jul 1, 2015, at 10:01 AM, Eric Pettersen <pett@cgl.ucsf.EDU> wrote:
Hi Alex, To get specifically get the second most probable rotamer you add the "criteria" keyword to the swapaa command with the value "2", e.g.: swapaa ASP :41.a criteria 2 You don't really say why you specifically want the second rotamer. Are you trying out all the rotamers one by one? You might want to consider doing that via the a Python script that uses the functions in the Rotamers module. That way you can find out how many rotamers are available, which isn't really possible with just the swapaa command. Another thing to consider is that if you know the chi angles you want, you can just swap to the new residue type and then request those specific chi values. For example to change residue 41.A to ASP and set its chis to 40 and 75:
swapaa ASP :41.a setattr a chi1 40 :41.a setattr a chi2 75 :41.a
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Jul 1, 2015, at 9:32 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Alex, Not directly, the “swapaa” command only uses the ranking rules that you tell it to use. Only if the rules happened to choose that rotamer would you get it. To directly choose a specific rotamer as listed in the rotamers dialog, you would have to use that dialog (Rotamers graphical user interface).
The rules are specified with the “criteria” option of swapaa, see: < http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/swapaa.html#criteria
Rotamers graphical interface: <
http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/rotamers/framerot....
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jul 1, 2015, at 4:57 AM, roz orchidea <roz.orchidea@gmail.com>
wrote:
Dear all, I would like to use swapaa and choose which rotamer I want. Foe
example I want from library dynameomics the second rotamer that appears in the pop-up menu of Arg. is it possible?
Thank you for your time, Alex
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (4)
-
Elaine Meng -
Eric Pettersen -
Repic Matej -
roz orchidea