- ChimeraX-users - RBVI Mailing Lists

About saving alphafold2 predictions
by Luz Cristina Vallejo Garcia 12 Oct '23

12 Oct '23

Hi there! I have a problem using ChimeraX. I tried to use the aphafold2 tool to predict a large protein structure. The process to predict the structure of my protein was successfully completed, but the downloading of my results failed. I observed that the folder for the prediction was created but is empty. So my questions are: Why did the program fail to download my results? Is there a possibility to obtain my results without to re-run the process? Thanks in advance Cris Vallejo IBt, UNAM, México <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Libre de virus.www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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saving alignment in ESP format using chimerax
by Ferreira Ramos, Ana Sofia 11 Oct '23

11 Oct '23

Hi, I would like to save a sequence alignment in ESP format but in my chimerax the option "Save EPS" is not present in the menu of the sequence viewer. The menu is only show if I right click inside the sequence viewer and I do not have all options there: [cid:55913c6a-a21d-45c9-b616-c60bdb4a6b4a] Please, could you let me know how can I save the alignment in the ESP format? Is there a way to do it through the command line? Thank you very much for your attention. Kind regards, Ana

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Re: [Chimera-users] ChimeraX Redistribution Policy Question
by Tom Goddard 10 Oct '23

10 Oct '23

Hi Pat, The ChimeraX license does not allow redistribution. But we have sometimes given permission for that, for example the Structural Biology Grid Consortium (SBGrid). The main issue is our project is funded almost entirely by grants and we have to document how widely the program is used to continue to get funding. Could you explain more details about your distribution? In what way does it use ChimeraX? Can ChimeraX visualization use desktop graphics rendering accelerated by the graphics card within in a Docker image? In general we recommend using ChimeraX on laptop/desktop computers, not containerized, not remotely displayed, because the interactive 3D rendering is often slow or broken in virtualized setups. Let's continue this discussion on the ChimeraX mailing list, not the Chimera mailing list. Tom > On Oct 8, 2023, at 5:53 PM, Patrick Rynkiewicz (RIT Student) via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello! > > I am a co-developer on a molecular dynamics software package that relies on UCSF ChimeraX, and am looking to package this software in a docker container. It's unclear to me from the licensing process what the policy is for ChimeraX redistribution, such as including the .deb package in a docker build. Can you please clarify if I would be able to cite and redistribute ChimeraX 1.6, Ubuntu 22.04 to non-commercial users in my software package, or does each individual user need to accept the non-commercial license agreement separately? > > Thanks! > > Pat Rynkiewicz > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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ChimeraX- protein protein interaction parameter
by Elaine Meng 05 Oct '23

05 Oct '23

Hi Ali, My colleague shared your question with me and I will try to answer it here. For the future, please send your ChimeraX questions to chimerax-users(a)cgl.ucsf.edu (CC'd here so you don't need to do anything this time) so that other users can benefit, unless you are including data that needs to be kept private. Sorry, ChimeraX does not calculate binding affinities (binding free energy) or predict their changes when you mutate the protein. You can only get a an approximate, first-order impression of whether they appear to improve or disrupt favorable interactions by measuring things like the surface area in the interface or the number of hydrogen bonds or clashes (bad packing) between the binding partners. See command "measure buriedarea" and the tools "Hbonds" "Contacts" and "Clashes" : <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#buriedarea> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/hbonds.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html> The picture that you get from these tools might still be incorrect if any of the 3D structures are predicted inaccurately (wrong sidechain conformations, wrong binding interface, wrong fold, etc.). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > From: Ali Aljasser <aljassera(a)cua.edu> > Subject: ChimeraX- protein protein interaction parameter > Date: October 5, 2023 at 5:12:46 PM PDT > > I am part of Dr. Choy's group at the Catholic University of America. I work on studying the protein-protein interaction for two kinetochore proteins. Based on alpha fold prediction, we utilized Chimerax to predict the strength of the interaction of these two proteins. We also added some mutations that are known to influence the interaction. However, I still struggling with how to find parameters such as delta G that would help me to predict the strength of the interaction and whether the mutations affect the interaction. > > Please let me know if you can assist me in this regard. Thank you for your time and I am looking forward to hearing from you soon. > Regards, > Ali

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Saving Looking Glass shots and movies
by tolung.bio＠gmail.com 05 Oct '23

05 Oct '23

Hi, Once I open a structure, create a scene and adjust the depth in the Looking Glass display, is there way to save that in a format that can then be imported into the Looking Glass Studio to be displayed in the stand-alone mode of the display? It is possible to do the same thing with animation, such as a 360 rotation or rocking? Thanks, Gökhan

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Surface representation - Dots
by Dennis Dannecker 04 Oct '23

04 Oct '23

Hello, I would like to ask a question regarding the surface representation of protein molecules in ChimeraX. I remember from Chimera that one could very customize the surface representation in terms of probe size, vertices density, and dot size used in the dot surface representation. While ChimeraX also allows to show dot surface representation, does it also allow for setting these attributes? But the more important question of mine is, can one export/extract the coordinates (spherical or cartesian) of the dots generated during dot surface representation. I would be interested in a file that holds the coordinates of these dots/particles around the molecule. In principal that should be possible, but as always, how amenable is that data? Thank you very much. Cheers Dennis

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Showing CAVER channels and tunnels
by Tom Goddard 03 Oct '23

03 Oct '23

I wrote a brief tutorial on how to show channels and tunnels computed by CAVER using ChimeraX. https://rbvi.github.io/chimerax-recipes/caver/caver.html Tom

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worm plots?
by Gabriel Lander 03 Oct '23

03 Oct '23

Is it by any chance possible to do b-factor worm plots in ChimeraX yet? I recall this was going to take a lot of effort since the code for ribbon depiction would have to be overhauled, but hoping maybe there's been some progress. If not I'll keep exporting from Chimera. thanks, -gabe

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Speeding up commands from cxc
by Alexander Hung Lee 02 Oct '23

02 Oct '23

Hello everyone, I'm working to automate making movies from 10,000 frame trajectories. Currently, my cxc contains the following commands windowsize 1920 1080 set bgColor white view zalign ligand inFrontOf #1 sel protein surface; surface color salmon; transparency protein 60 target s sel :UNL color sel dark slate gray; color sel byhetero sel :SIA color sel dim gray; color sel byhetero sel :UNL hbonds :UNL reveal true surface zone #1 nearAtoms ligand distance 15 select zone ligand 15; select add ligand select ~sel ~cartoon sel delete sel ~sel view ligand movie record supersample 4 perframe "~label; label hbondatoms" ; coordset #1 1,10000,50; wait 200; ~perframe movie encode output hbond.mp4 bitrate 6000 framerate 4 The above takes ~ 30 mins, and it's something I would like to do for whole libraries I'm screening. I think the longest process is "hbonds :UNL reveal true" while second longest is movie record and perframe. Is there a way to speed this up? Is there a way to take advantage of multi-threading if it isn't already enabled? If multi-threading is already being used, what can I change to be more efficient? I deleted the parts that I didn't need "delete sel" since they're not involved in the binding site, and I thought it would help speed up surface calculations while recording. Regards, Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

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Bright light while using fly command
by Haselbach,David 02 Oct '23

02 Oct '23

Hi, I am trying to make a fly movie in which I move from one rotation state of the molecule to the next. Unfortunately, the lighting during the flight is not nice. The light goes very bright while moving and in the end jumps back to normal. However, if I do the turn life with mouse the light is fine. I am using soft lighting. Find attached an example movie. What could I do? Can anyone help? Best, David

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