- ChimeraX-users - RBVI Mailing Lists

memory questions
by Tintos-hernandez, Alonso A 18 Oct '23

18 Oct '23

Hi i was trying to do some modeling using the alfafold colab but it says that i need to buy more memory to run more modeling, hos should i do that ? Jesus Tintos Childrens Hospital of Philadelphia Senior scientist II

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model becomes invisible behind the map when color with hexadecimal color codes
by Kai Cai 17 Oct '23

17 Oct '23

Hi, I've got this weird bug that hope you can help me with. When I try to color a selected protein model with nonmajor hexadecimal color codes (e.g. #f17d21cc), the selected model will become invisible behind the map it was fit with. The map is set as transparent surface. Once it becomes invisible, it won't come back no matter how I change the color. This appears to be a recent issue. Not sure if it's a bug caused by recent macOS update. I am running the most recent ChimeraX daily update on a macOS 14.0. Here is an example if you would like to test it: open 25428 fromDatabase emdb open 7sth transparency 50 select #2 color sel #f17d21cc Thanks, Kai ________________________________ UT Southwestern Medical Center The future of medicine, today.

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Opening series of pdb's in incorrect sequential order
by Alexander Hung Lee 13 Oct '23

13 Oct '23

I have a series of pdb's in a folder numbered 1 - 500 (so 1.pdb ... 500.pdb). I'm opening them in ChimeraX using *.pdb. I'm expecting 1.pdb to have ID1 and 2.pdb to to be ID2, but it appears ChimeraX is only looking at the first digit and not the whole number. Is there a way around this? For now, my work around is to use 001, 002 ... 500 instead [cid:d19d2d17-71bb-430f-8a09-65921a0ca962] 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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Gaussian surface visualization of a subset of residues
by Stefano Pellegrini 13 Oct '23

13 Oct '23

To whom it may concern, I am a PhD student at the Biomedical Genomics Lab at the Institute of Biomedicine of Barcelona. I am using ChimeraX to produce figures for the publication of an in-house recently developed tool for cancer driver gene discovery. I am new to using ChimeraX, so I am sorry if my question might seem very naive to you. Anyway, I can't find this information anywhere else. My problem is simple: I want to show the surface (or volume) occupied by the atoms of a selected number of residues within a chain. I can easily achieve this by using the Gaussian surface (GS) by adding the parameter "resolution" to the "surface" command as "surface :10-20 resolution 6" The problem is that the surface visualized in this way has "gaps" where it overlaps with other atoms that are not from the selected residues. As expected, these gaps get larger when using a greater resolution. Now, I would like to show the complete surface around these residues, without gaps. Could you please provide any suggestions? Thank you in advance, and best regards, Stefano Pellegrini -- *Stefano Pellegrini, **PhD student* Barcelona Biomedical Genomics Lab Institute for Research in Biomedicine (IRB) Carrer de Baldiri Reixac 10, 08028, Barcelona, Spain http://bbglab.irbbarcelona.org

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About saving alphafold2 predictions
by Luz Cristina Vallejo Garcia 13 Oct '23

13 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 11 Oct '23

11 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 06 Oct '23

06 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 04 Oct '23

04 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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ChimeraX Alphafold Question
by Vincent Candela 02 Oct '23

02 Oct '23

Hello, I am an undergraduate researcher at McGill University using the Alphafold feature of ChimeraX to study the role of tau on microtubule dimers, and I was wondering if you could point me to detailed documentation on the energy-minimization feature of Alphafold. I’ve been looking at the ChimeraX documentation and couldn’t find an in-depth documentation on what it does. Thank you so much, Vincent Candela

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Color info
by Margulies, David (NIH/NIAID) [E] 29 Sep '23

29 Sep '23

If I color, say, “bychain” how do I get the info on what the displayed color is. Is there an info color command? David H. Margulies, MD, PhD Chief, Molecular Biology Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health Bldg. 10; Room 11D12 10 Center Drive Bethesda, MD 20892-1892 Email: dmargulies(a)niaid.nih.gov<mailto:dmargulies@niaid.nih.gov>, dhm(a)nih.gov<mailto:dhm@nih.gov> Ph: 301-496-6429 Fax: 301-480-7352 Web: https://www.niaid.nih.gov/research/david-margulies-md-phd “Public service is a public trust, requiring employees to place loyalty to the Constitution, the laws, and ethical principles above private gain.” – executive order 12674, https://www.federalregister.gov/documents/2016/02/17/2016-03214/standards-o…<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.federalregister.go…> Disclaimer: The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender’s own and not expressly made on behalf of the NIAID by one of its representatives.

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wildcard used within SAVE command
by 洪冉 29 Sep '23

29 Sep '23

Hi all, I have been trying to produce some high-resolution pictures recently using ChimeraX. And "save C:/xxxx/xxxx/test.png" was used to produce the pic, then I had to change the context "test" into each structure name manually. e.g. save C:/xxxx/xxxx/benzene.png or save C:/xxxx/xxxx/methanol.png Actually, the structure loaded into chimeras was with the right name. Hence, I want to ask for help if is there a wildcard that could be used in the "save" command for saving the picture with the name of the structure. e.g. save C:/xxxx/xxxx/${nameofstruc}.png Of course, it does not work. I just want to give this as an example to suggest my opinions. Thanks in advance. Yours, Ran

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How to activate the Extract button in Segment Map function?
by Bo Chen 25 Sep '23

25 Sep '23

Dear ChimeraX, I tried to use Segment Map to remove some portions of the cryoEM map, and extract the selected portion, but the extract button remains shaded. The only tab in the "other tools" row that appears to be activated is "Fit". I have the most recent version of ChimeraX installaed(Sept 19). Could you give me some hints how to activate the extract in "Other tools" under the "Shortcut options" in "Segment Map"? Thanks! Bo

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Changing mesh size to save as STL file
by Arthur Melo 25 Sep '23

25 Sep '23

Dear colleagues, Is there a way to refine or decimate a mesh of a map to save as an STL file? All the best, Arthur

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symmetrizing the model
by Dmitry Semchonok 22 Sep '23

22 Sep '23

Dear colleagues, A very quick question - what is the command to apply the symmetry to the 3D model? (please provide a usage example if possible). Will the soft generate the symmetrized model after this command application? I found the one for Chimera but not for ChimeraX. Many thanks. Sincerely, Dmitry

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Equivalents to sop split & mask?
by Oliver Clarke 21 Sep '23

21 Sep '23

Hi, Is there a direct equivalent to the command “sop split” in ChimeraX? In the documentation for the “surface” command, I can see that there is an option to split by color, but not to split into individually selectable blobs. We use this a lot in Chimera, as a quick way to make a starting point for a mask to use in refinement, so it would be great to have in ChimeraX too. Also, is there an equivalent to the “mask” command from Chimera? I can’t seem to find it but perhaps it has a different name? Cheers Oli

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Labels of selected residues even with their model name
by svle＠tiscali.it 21 Sep '23

21 Sep '23

Hi, I have used matchmaker with four loaded models to compare the side chains orientation of some selected residues. It is possible to label the selected residues even with the information of the model name they belong to? Thanks. Saverio

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Open and play volume series in ChimeraX
by Wout Oosterheert 20 Sep '23

20 Sep '23

Dear ChimeraX team, I’m currently trying to open a volume and play a volume series in ChimeraX. According to the website (https://www.cgl.ucsf.edu/chimerax/docs/user/trajectories.html) opening a volume series should work like this: “Volume data can be opened as a series with open, employing filename wildcard symbols or globbing as needed to specify multiple files in a single command”. This seems simple enough, I indeed can open the volumes as a group. However, when I then try to play the series using: vseries play #1 direction oscillate loop true, I get the error: no volume series specified. Could you explain to me how I can get my group of volumes recognized as a volume series? The vseries page (https://www.cgl.ucsf.edu/chimerax/docs/user/commands/vseries.html) is very elaborate, but I cannot find alternative options of opening my volumes as a series. I know how to do things in regular Chimera, but would prefer to stick with ChimeraX because I make all my other figures with it. Thank you very much in advance!! Best, Wout Wout Oosterheert, PhD Humboldt Postdoctoral Fellow Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund, Germany Phone +49-(0)231-133-2357 Email: wout.oosterheert(a)mpi-dortmund.mpg.de<mailto:wout.oosterheert@mpi-dortmund.mpg.de>

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seq_rmsd and align command
by dng26＠mrc-mbu.cam.ac.uk 19 Sep '23

19 Sep '23

Hello, I have two PDB models I am comparing, but I am having some issues generating the seq_rmsd attribute across all of the chains in the superposition that I want. My current models (same protein, but different states and slightly altered built sequences) have chains A/B/C/D/E/F separated over two domains of A/B/C and D/E/F, for example. My problem is that domain D/E/F is much larger than the former and when I run a matchmaker command such as this: matchmaker #1/A/B/C/D/E/F to #2/A/B/C/D/E/F pairing ss show true I get the resulting superposition favoring the /D/E/F domain (larger RMSD values on A/B/C). This would be fine, however, I want to investigate RMSD variation in D/E/F relative to a fixed position of A/B/C. If I run the following command I only get pairwise RMSDs (seq_rmsd header) for the specified chains but lack those of the larger D/E/F domain as they are not included. matchmaker #1/A/B/C to #2/A/B/C pairing ss show true I look to Calculate the RMSD between paired residues of chains /A/B/C/D/E/F without moving the current structures (after ‘mmaker’ alignment to A/B/C) with the ‘align’ command but the ‘move’ option set to nothing: align #1/A/B/C/D/E/F toAtoms #2/A/B/C/D/E/F move nothing matchNumbering (or matchAtomNames also tested) true I believe the above is what I want with regards to superposition for the RMSD calculations, but the ‘align’ job does not appear to give a seq_rmsd header attribute once run, even though the log seems to suggest it does a pairwise residue alignment to calculate the RMSDs. (Possibly because it does not just look at the CA like matchmaker does?) Is there a way to generate seq_rmsd attributes from the ‘align’ command, or is there a way to have an equivalent ‘move nothing’ in ‘mmaker’? I am looking to use seq_rmsd information to color the model and I am using v1.6.1. Any help is much appreciated! Dan.

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Chimerax
by François Ferron 15 Sep '23

15 Sep '23

Hi I am making a figure using a pdb and a density map in chimeraX1.6.1. each time I do that I have coloured arrows representing an axis that is in the middle. how do I get rid of them. I am sure it is trivial but I just could not find the answers in the manual. thanks François -- François Ferron, Ph.D. francois.ferron(a)univ-amu.fr @F2erron@fediscience.org Laboratoire CNRS - UMR 7257 (AFMB) AFMB - POLYTECH Case 925 163, Av de Luminy 13288 Marseille Cedex 09 France & European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany ######################################### Success is not final, failure is not fatal; it's the courage to continue that counts.

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