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<p class="MsoNormal"><span style="font-size:11.0pt">Thanks a lot Dr. Meng. FYI, Is there any example script I can use as an example for using BILD to write PCA arrows?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Tianming<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Date: </b>Wednesday, February 8, 2023 at 11:39 AM<br>
<b>To: </b>Tianming Qu <tqu@fsu.edu><br>
<b>Cc: </b>ChimeraX Users Help <chimerax-users@cgl.ucsf.edu><br>
<b>Subject: </b>Re: [chimerax-users] About plotting independent component analysis vectors<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:11.0pt">Hi Tianming,<br>
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:<br>
<br>
<https://urldefense.com/v3/__https://rbvi.ucsf.edu/chimerax/docs/user/formats/bild.html__;!!PhOWcWs!y99spJ5YELIwhLj_bQHW9Wx6Jxc7Q7ZrcCeSChNqSTdjMZlZseIHjuEKVsqThLUWs-t7tAvNSEChWA$ ><br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
> On Feb 8, 2023, at 8:36 AM, Tianming Qu via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> <br>
> Hi Dr. Meng,<br>
> <br>
> 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.<br>
> <br>
> Best,<br>
> Tianming<br>
> <br>
> From: Elaine Meng <meng@cgl.ucsf.edu><br>
> Date: Wednesday, February 8, 2023 at 11:33 AM<br>
> To: Tianming Qu <tqu@fsu.edu><br>
> Cc: Tianming Qu via ChimeraX-users <chimerax-users@cgl.ucsf.edu><br>
> Subject: Re: [chimerax-users] About plotting independent component analysis vectors<br>
> <br>
> Hi Tianming,<br>
> 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.
<br>
> Best,<br>
> Elaine<br>
> -----<br>
> Elaine C. Meng, Ph.D. <br>
> UCSF Chimera(X) team<br>
> Department of Pharmaceutical Chemistry<br>
> University of California, San Francisco<br>
> <br>
> > On Feb 8, 2023, at 8:00 AM, Tianming Qu via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:<br>
> > <br>
> > Dear all, <br>
> > <br>
> > 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.<br>
> > <br>
> > Best,<br>
> > Tianming<br>
> <br>
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<o:p></o:p></span></p>
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