About plotting independent component analysis vectors
Dear all,
Is there any way I can display the eigenvectors I got from the independent component analysis on ChimeraX, which is calculated from the protein MD trajectory.
Best, Tianming
Hi Tianming, I do not know which calculation you are talking about. As far as I know, ChimeraX does not have any option to calculate independent components from an MD trajectory. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2023, at 8:00 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear all,
Is there any way I can display the eigenvectors I got from the independent component analysis on ChimeraX, which is calculated from the protein MD trajectory.
Best, Tianming
Hi Dr. Meng,
I have the independent components calculated already, sorry I did not make myself clear. I am wandering if I can use ChimeraX to display the ICA results I got from my own calculation.
Best, Tianming
From: Elaine Meng meng@cgl.ucsf.edu Date: Wednesday, February 8, 2023 at 11:33 AM To: Tianming Qu tqu@fsu.edu Cc: Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] About plotting independent component analysis vectors Hi Tianming, I do not know which calculation you are talking about. As far as I know, ChimeraX does not have any option to calculate independent components from an MD trajectory. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2023, at 8:00 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear all,
Is there any way I can display the eigenvectors I got from the independent component analysis on ChimeraX, which is calculated from the protein MD trajectory.
Best, Tianming
Hi Tianming, There is no built-in option to read ICA vectors calculated by some other program. You may be able to script it yourself, e.g. by creating 3D arrows in BILD format or something like that. BILD format is a simple text input file described here:
https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2023, at 8:36 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Dr. Meng,
I have the independent components calculated already, sorry I did not make myself clear. I am wandering if I can use ChimeraX to display the ICA results I got from my own calculation.
Best, Tianming
From: Elaine Meng meng@cgl.ucsf.edu Date: Wednesday, February 8, 2023 at 11:33 AM To: Tianming Qu tqu@fsu.edu Cc: Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] About plotting independent component analysis vectors
Hi Tianming, I do not know which calculation you are talking about. As far as I know, ChimeraX does not have any option to calculate independent components from an MD trajectory. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2023, at 8:00 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear all,
Is there any way I can display the eigenvectors I got from the independent component analysis on ChimeraX, which is calculated from the protein MD trajectory.
Best, Tianming
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks a lot Dr. Meng. FYI, Is there any example script I can use as an example for using BILD to write PCA arrows?
Best, Tianming
From: Elaine Meng meng@cgl.ucsf.edu Date: Wednesday, February 8, 2023 at 11:39 AM To: Tianming Qu tqu@fsu.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] About plotting independent component analysis vectors Hi Tianming, There is no built-in option to read ICA vectors calculated by some other program. You may be able to script it yourself, e.g. by creating 3D arrows in BILD format or something like that. BILD format is a simple text input file described here:
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/formats... >
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2023, at 8:36 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Dr. Meng,
I have the independent components calculated already, sorry I did not make myself clear. I am wandering if I can use ChimeraX to display the ICA results I got from my own calculation.
Best, Tianming
From: Elaine Meng meng@cgl.ucsf.edu Date: Wednesday, February 8, 2023 at 11:33 AM To: Tianming Qu tqu@fsu.edu Cc: Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] About plotting independent component analysis vectors
Hi Tianming, I do not know which calculation you are talking about. As far as I know, ChimeraX does not have any option to calculate independent components from an MD trajectory. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2023, at 8:00 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear all,
Is there any way I can display the eigenvectors I got from the independent component analysis on ChimeraX, which is calculated from the protein MD trajectory.
Best, Tianming
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...https://urldefense.com/v3/__https:/www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users__;!!PhOWcWs!y99spJ5YELIwhLj_bQHW9Wx6Jxc7Q7ZrcCeSChNqSTdjMZlZseIHjuEKVsqThLUWs-t7tAtJjkTBOg$
Hi Tianming, I meant to just create the BILD file(s) directly. It is a very simple plain-text format described in the help page, which also links to example BILD files that include arrows. Details of how to do it (or script it) would depend on the format that you have now, which we don't know anything about. In ChimeraX, you just open the bild file to show the objects.
https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2023, at 8:46 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thanks a lot Dr. Meng. FYI, Is there any example script I can use as an example for using BILD to write PCA arrows?
Best, Tianming
From: Elaine Meng meng@cgl.ucsf.edu Date: Wednesday, February 8, 2023 at 11:39 AM To: Tianming Qu tqu@fsu.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] About plotting independent component analysis vectors
Hi Tianming, There is no built-in option to read ICA vectors calculated by some other program. You may be able to script it yourself, e.g. by creating 3D arrows in BILD format or something like that. BILD format is a simple text input file described here:
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/formats... >
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2023, at 8:36 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Dr. Meng,
I have the independent components calculated already, sorry I did not make myself clear. I am wandering if I can use ChimeraX to display the ICA results I got from my own calculation.
Best, Tianming
From: Elaine Meng meng@cgl.ucsf.edu Date: Wednesday, February 8, 2023 at 11:33 AM To: Tianming Qu tqu@fsu.edu Cc: Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] About plotting independent component analysis vectors
Hi Tianming, I do not know which calculation you are talking about. As far as I know, ChimeraX does not have any option to calculate independent components from an MD trajectory. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2023, at 8:00 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear all,
Is there any way I can display the eigenvectors I got from the independent component analysis on ChimeraX, which is calculated from the protein MD trajectory.
Best, Tianming
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Dear Elaine, Tianming and everyone else,
I have now written a function for ProDy for writing bild files for these kinds of modes of motion (see https://github.com/prody/ProDy/pull/1658). It is very easy to add this kind of data to a ProDy object to use it (see https://github.com/prody/ProDy/issues/1656).
Best wishes James
Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu escribió:
Hi Tianming, I meant to just create the BILD file(s) directly. It is a very simple plain-text format described in the help page, which also links to example BILD files that include arrows. Details of how to do it (or script it) would depend on the format that you have now, which we don't know anything about. In ChimeraX, you just open the bild file to show the objects.
https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html
Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2023, at 8:46 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thanks a lot Dr. Meng. FYI, Is there any example script I can use as an example for using BILD to write PCA arrows?
Best, Tianming
From: Elaine Meng meng@cgl.ucsf.edu Date: Wednesday, February 8, 2023 at 11:39 AM To: Tianming Qu tqu@fsu.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] About plotting independent component analysis vectors
Hi Tianming, There is no built-in option to read ICA vectors calculated by some other program. You may be able to script it yourself, e.g. by creating 3D arrows in BILD format or something like that. BILD format is a simple text input file described here:
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/formats...
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2023, at 8:36 AM, Tianming Qu via ChimeraX-users
chimerax-users@cgl.ucsf.edu wrote:
Hi Dr. Meng,
I have the independent components calculated already, sorry I did
not make myself clear. I am wandering if I can use ChimeraX to display the ICA results I got from my own calculation.
Best, Tianming
From: Elaine Meng meng@cgl.ucsf.edu Date: Wednesday, February 8, 2023 at 11:33 AM To: Tianming Qu tqu@fsu.edu Cc: Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] About plotting independent
component analysis vectors
Hi Tianming, I do not know which calculation you are talking about. As far as
I know, ChimeraX does not have any option to calculate independent components from an MD trajectory.
Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2023, at 8:00 AM, Tianming Qu via ChimeraX-users
chimerax-users@cgl.ucsf.edu wrote:
Dear all,
Is there any way I can display the eigenvectors I got from the
independent component analysis on ChimeraX, which is calculated from the protein MD trajectory.
Best, Tianming
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription:
https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi James, Great! Thanks for creating this and making it available to ChimeraX users.
Users may want to check out the ProDy website to get a better idea of what it is/does: http://prody.csb.pitt.edu/
Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 9, 2023, at 12:19 PM, JAMES MICHAEL KRIEGER jmkrieger@cnb.csic.es wrote:
Dear Elaine, Tianming and everyone else,
I have now written a function for ProDy for writing bild files for these kinds of modes of motion (see https://github.com/prody/ProDy/pull/1658). It is very easy to add this kind of data to a ProDy object to use it (see https://github.com/prody/ProDy/issues/1656).
Best wishes James
Elaine Meng via ChimeraX-users chimerax-users@cgl.ucsf.edu escribió:
Hi Tianming, I meant to just create the BILD file(s) directly. It is a very simple plain-text format described in the help page, which also links to example BILD files that include arrows. Details of how to do it (or script it) would depend on the format that you have now, which we don't know anything about. In ChimeraX, you just open the bild file to show the objects.
https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html
Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2023, at 8:46 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Thanks a lot Dr. Meng. FYI, Is there any example script I can use as an example for using BILD to write PCA arrows?
Best, Tianming
From: Elaine Meng meng@cgl.ucsf.edu Date: Wednesday, February 8, 2023 at 11:39 AM To: Tianming Qu tqu@fsu.edu Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] About plotting independent component analysis vectors
Hi Tianming, There is no built-in option to read ICA vectors calculated by some other program. You may be able to script it yourself, e.g. by creating 3D arrows in BILD format or something like that. BILD format is a simple text input file described here:
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/formats... >
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2023, at 8:36 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Dr. Meng,
I have the independent components calculated already, sorry I did not make myself clear. I am wandering if I can use ChimeraX to display the ICA results I got from my own calculation.
Best, Tianming
From: Elaine Meng meng@cgl.ucsf.edu Date: Wednesday, February 8, 2023 at 11:33 AM To: Tianming Qu tqu@fsu.edu Cc: Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] About plotting independent component analysis vectors
Hi Tianming, I do not know which calculation you are talking about. As far as I know, ChimeraX does not have any option to calculate independent components from an MD trajectory. Best, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 8, 2023, at 8:00 AM, Tianming Qu via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Dear all,
Is there any way I can display the eigenvectors I got from the independent component analysis on ChimeraX, which is calculated from the protein MD trajectory.
Best, Tianming
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/mailman/listinfo/chime...
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Elaine Meng -
JAMES MICHAEL KRIEGER -
Tianming Qu