- ChimeraX-users - RBVI Mailing Lists

Reverse color byhet
by Ahmad Khalifa 13 Feb '20

13 Feb '20

If I color byhet then color zone a volume, the volume takes some colors from the hetero atom colors. How to reverse byhet coloring? Regards.

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select menu bundle tags
by Anthony James Schaefer 12 Feb '20

12 Feb '20

Hello Are there any plans to add bundle tags for putting selectors on the select menu? Thanks, Tony

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Color by Conservation in ChimeraX
by Sean Moore 11 Feb '20

11 Feb '20

Hello, I read an older post that color by conservation is pending for ChimerX. Is it available now? When I open a sequence alignment that I generated elsewhere, it shows the alignment and conservation, it identified the correct protein chain, but there is no menu in that window to assign the colors to the protein. (no option to "Again from the Multalign Viewer menu, choose: Structure... Render by Conservation. This will call Render by Attribute, in which…”) Should I use Chimera for this instead of ChimeraX? Sean

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Reproduce exact view
by Christophe Leterrier 10 Feb '20

10 Feb '20

Hi, I haven't been able to find how to - log - set - store - recall a precise view (ie get the same exact image if I do a snapshot). First use case would within the same session (fixed computer, window size, no restart of the application in between). Second use case (more tricky?) would be independently of computer / window size / current session. Thanks for your help! Christophe

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Re: [chimerax-users] Crossfade rough transition while making a movie
by Elaine Meng 07 Feb '20

07 Feb '20

Hi Ahmad, This appearance of snapping to the position may not be very avoidable, because “view” transitions just take a linear path and it always looks somewhat abrupt (to me anyway) when it reaches the endpoint. There is currently no option to make it go slower when it is closer to the end. You could try saving an additional position along the way and using it as an intermediate and then going slower after the intermediate by using more frames per distance, and/or you could try adding a few extra wait frames between when it reaches the endpoint and when it starts the crossfade, for example: view pos6 50; wait 100 crossfade 50; view pos5; wait 50 (OR: crossfade 50 viewpos5 50; wait 50) However, I don’t know if either of those would help much. When I’m making a movie I usually end up experimenting a lot with numbers of frames in movements and waits, but the sharp endpoints of view transitions are not currently avoidable as I understand it. Best, Elaine > On Feb 7, 2020, at 1:10 PM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > Hi Elaine, > > Sorry if my description was vague. With the modification you suggested, I still have the rough transition between pos6 and pos5 but with a slower crossfade into pos5. > > I attached my movie (made with script in the original post) to get a better idea of what I mean. At 0:2, pos6 appears like it snaps in place, then the crossfade into pos5 occurs. > > Is there a way to make the transition smoother? > > Regards. > > On Fri, Feb 7, 2020 at 12:18 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hi Ahmad, > Not sure I understand what you actually want, but I’ll try to answer anyway… > > If you mean you want to see a gradual change in position from pos6 to pos5 then you would need to put a frames number after pos5, for example: > > crossfade 50; view pos5 50; wait 50 > > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#name> > > (Crossfade does not interpolate the movement, you have to do it with the view command.) > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/crossfade.html> > > Some minor notes on scripts. You do not need “;” at the end of any line; it is only needed to separate commands that are on the same line as each other, as in the example above. > <http://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-…> > > 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 6, 2020, at 11:59 PM, Ahmad Khalifa <underoath006(a)gmail.com> wrote: > > > > I want to crossfade pos6 into pos5, the crossfading itself is smooth, but the below script gives me an abrupt transition at the start of the crossfade (at pos6), how can I fix that?! > > > > view pos4 > > wait 30; > > > > movie record supersample 3 size 1920,1080 > > view pos6 50 > > wait 50; > > crossfade 50; view pos5 > > wait 50; > > movie encode IJ_movie3.mp4 quality high > > <IJ_movie3.mp4>

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Crossfade rough transition while making a movie
by Ahmad Khalifa 07 Feb '20

07 Feb '20

I want to crossfade pos6 into pos5, the crossfading itself is smooth, but the below script gives me an abrupt transition at the start of the crossfade (at pos6), how can I fix that?! view pos4 wait 30; movie record supersample 3 size 1920,1080 view pos6 50 wait 50; crossfade 50; view pos5 wait 50; movie encode IJ_movie3.mp4 quality high

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Command line interface is detached
by Ahmad Khalifa 04 Feb '20

04 Feb '20

My command line interface used to be attached at the bottom. Now it's floating on the screen and the only way I could attach it back is to place it in the right panel. How can I attach it back to the bottom of the screen, spanning the entire length of the ChimeraX window? P.s. I'm running Linux Centos 7.

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Chimerax on a HPC cluster
by Thu Nguyen 31 Jan '20

31 Jan '20

Dear all, I administer a small HPC cluster (Rocks 7) at a bio research institute and a user has requested Chimerax to be installed on it. Has anyone successfully done so ? If yes, I wish to help some hints as to how it is done and an assessment of how it performs . Thanks and regards Thu D. Nguyen Systems & Computational Biology Platform Bio21 Molecular Sciences and Biotechnology Institute, University of Melbourne www.bio21.org

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question about ChimeraX Hide Dust Feature
by Philip Schmiege 29 Jan '20

29 Jan '20

Hi I just downloaded the new ChimeraX, and was wondering where the Hide Dust option is located. I cannot find it. Any help is greatly appreciated! Philip _____________________________________ Philip Schmiege Graduate Student in Biophysics Li Lab, Dept. of Molecular Genetics, L5.162 philip.schmiege(a)utsouthwestern.edu ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Fwd: Colors from snapshots
by Christophe Leterrier 29 Jan '20

29 Jan '20

Hi, I wonder why the colors in the snapshots (and movies) from ChimeraX are always washed-out compared to the colors I get live in the viewer. Attached is a screenshot with the viewer on the left, the corresponding snapshot on the right: one can see how the snapshot is desaturated compared to the viewer. From my limited tests it is the case when saving as both PNG and PPM, and I wonder if this could be corrected. I could saturate the screenshots afterward but it doesn't seem right to me to grossly mess with color levels post-hoc given how stunning the shaded rendering from ChimeraX are. Thanks, Christophe

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