[chimerax-users] About plotting independent component analysis vectors

[JAMES MICHAEL KRIEGER]

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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