[chimerax-users] About plotting independent component analysis vectors

[Elaine Meng]

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 at 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 at 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 at 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 at cgl.ucsf.edu>
>>> Date: Wednesday, February 8, 2023 at 11:39 AM
>>> To: Tianming Qu <tqu at fsu.edu>
>>> Cc: ChimeraX Users Help <chimerax-users at 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/bild.html__;!!PhOWcWs!y99spJ5YELIwhLj_bQHW9Wx6Jxc7Q7ZrcCeSChNqSTdjMZlZseIHjuEKVsqThLUWs-t7tAvNSEChWA$ >
>>> 
>>> 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 at 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 at cgl.ucsf.edu>
>>> > Date: Wednesday, February 8, 2023 at 11:33 AM
>>> > To: Tianming Qu <tqu at fsu.edu>
>>> > Cc: Tianming Qu via ChimeraX-users <chimerax-users at 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 at 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
>>> >
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