- ChimeraX-users - RBVI Mailing Lists

Feature suggestions for the Segmentations tool
by Ricardo Righetto 27 Jun '24

27 Jun '24

Hi, Thanks a lot for adding the Segmentations mode in v1.8, this is very much welcomed for cryo-ET data! Are there any plans for expanding the capabilities of this tool? If possible, I would like to suggest some features for manual segmentation: * Segment contiguous density in 3D by clicking on it (akin to the blob selector in the "Right Mouse" options, which operates on surfaces) * Related: threshold-based segmentation i.e. segment in 3D all contiguous density between selected minimum and maximum density thresholds * 2D/3D Lasso-based segmentation * Dilation, erosion and smoothening of segmentations Some of these things are already possible by combining volume and surface operations or with external tools, but it would be very nice to have everything streamlined in one click (or a few) through the GUI. Alternatively, I would appreciate pointers on how to implement these features as a ChimeraX plugin. Happy to discuss more. Thank you and have a nice weekend! -- Ricardo Diogo Righetto

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Re: ChimeraX does not Support .stl files?
by Zach Pearson 26 Jun '24

26 Jun '24

Hi Kevin, Please direct questions about ChimeraX to our mailing list, chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> — others on the team or even in the community may have more experience or more recent experience in a given subject than I or any other developer has at the moment. Eric (CC’ed) has been working on the NIH 3D pipeline; part of that pipeline is adding struts to delicate objects for 3D printing. He may be able to help you better than I can. — Zach > On 26 Jun 2024, at 14:55, Maroney, Kevin James <kmaroney(a)uab.edu> wrote: > > Hello Dr. Pearson, > Despite doing more Immunology research and really no proteomics, I have had a hobby interest in fooling around with Pymol and ChimeraX. I just recently got a very nice 3D Printer and was hoping to print out a model of the epitope of my PhD complexed between HLA-B57 and TCR that is publically available. I was going to use UCSF Chimera, but it does not seem like it is capable of representing space-filling diagrams and only gives me errors. I obviously can’t print the complex and delicate ribbon or atomic representations and like ChimeraX better anyway. But the guide from the NIH suggests passing PDB models through Chimera to generate .stl files which I can easily then pop into my Studio software to 3D print and resize etc. Problem is, I don’t see that there is any way to actually export as .stl in ChimeraX. Is there any way you could add this feature? Thank you very much. Lovely program. > > Sincerely, > Kevin Maroney > M.S. Biotechnology > University of California, Irvine > PhD Student > University of Alabama at Birmingham

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transparency using in movie making
by Yanhe Zhao 26 Jun '24

26 Jun '24

Dear ChimeraX team, I have a map with model docking and am making movie. My plan is to fade away the map to show the docked model for next step. I tried the crossfade which works. But I want to use the transparency command for this purpose because I want to keep the map at specific transparency level, like 80%. The chimera has command like 'surftransparency 80 #1 50'. I was wondering what is the similar command in ChimeraX? Thanks and cheers, Yanhe

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Sequence based selections
by Kumpula, Esa-Pekka 26 Jun '24

26 Jun '24

Dear ChimeraX team, Two selection-related questions: 1. I'm looking for a way to combine multiple sequence based selections into one selection but I wasn't able to find a way to do this. The use case is, I have a lot of models that have these two proteins and I would like to use them together for superposition (via align command against Calphas). I would normally refer to them by chain ID, but here these are not consistently assigned so I need to use the sequence for selection. 1. Is it possible to have a named, sequence-based selection that, when called, would perform the selection? This would save a lot of pain when writing scripts for sequence based selections. Cheers, EP -- Esa-Pekka Kumpula, PhD Senior Postdoctoral Researcher Laboratory of Structural Biology Institute of Biotechnology Helsinki Institute of Life Science HiLIFE University of Helsinki www.helsinki.fi/lsb<http://www.helsinki.fi/lsb>

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Generic Linux installation package for ChimeraX 1.8
by Kumpula, Esa-Pekka 26 Jun '24

26 Jun '24

Dear ChimeraX team, I noticed that version 1.8 no longer comes with a "Generic Linux" installation package (unlike 1.7). I have been using this for a centralised installation on a network drive that has so far worked very well. Is this coming to 1.8 or is it discontinued? Cheers, Esa-Pekka -- Esa-Pekka Kumpula, PhD Senior Postdoctoral Researcher Laboratory of Structural Biology Institute of Biotechnology Helsinki Institute of Life Science HiLIFE University of Helsinki www.helsinki.fi/lsb<http://www.helsinki.fi/lsb>

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Bundles with dependencies
by Vincent Mallet 24 Jun '24

24 Jun '24

Hello, Thanks for the tool and the tutorials. I have a machine learning tool based on pytorch to analyse cryo-EM data. I was hoping to package (bundle) it for Chimerax and started to follow tutorials, but I don't think you mention the right way to set up a code environment with depencies. I see a numpy import in the save_new_format tutorial, but it's not listed in the "dependencies" section of the xml file. I guess my question is : can I add arbitrary packages in a bundle ? Is there a way to install pip packages only ? Should I copy all source code in the folder and deal with my imports like that ? In particular, I am thinking of torch that is not so easy to replace... I am hoping you can help me, thanks in advance for the help ! Best, Vincent

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Troubleshooting MOLE Channel Visualizations
by Josh Gonzalez 24 Jun '24

24 Jun '24

Hello, I am a newer user of ChimeraX and am having some trouble creating visualizations to characterize a channel of interest. I began by following the procedure outlined in the tutorial "MOLE Channel Coloring by Property" but quickly ran into some issues with my own channel. This led me to try the click-to-execute links for the example in the tutorial and I ran into the same problem. It seems ChimeraX cannot accept .json files that are not Alphafold PAE maps, meaning there is no way to visualize the results of the MOLEsever analysis. I have attempted parsing data from the .json into a usable file format such as a .bild or a .pdb in a separate anaconda kernel, and while I am able to get coordinates for a superimposed visualization, they are not selectable atoms that can be color-coded or manipulated as they are in the procedures following the "open molepore-1bl8.json" command. I know this is because I have not found a way to parse all of the useful data from the .json file into another format, but I do not see exactly how I would go about doing so. Is there a way to get ChimeraX to accept a .json file that is not a PAE plot without the need for parsing data or changing format? Thank you so much for the help!

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Question
by Suwisanto, Natasha 24 Jun '24

24 Jun '24

Hello, My name is Natasha Suwisanto. I’ve been using UCSF Chimera X and AlphaFold servers for a personal research project to mutate a GPCR protein. I just had a quick question. I was mutating a structure using the Rotamer tool on ChimeraX. I mutated a single amino acid (Tyrosine) to a Proline using the Richardson Common Atom library. However, when I ran AlphaFold on it, the predicted 'best model' structure they gave me had a different amino acid (Leucine) on the position I previously mutated the Tyrosine to the Proline. I was just wondering if I did something wrong or if AlphaFold/ChimeraX works differently than I thought. Best, Natasha Suwisanto

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Installing ChimeraX on Linux without sudo
by Ricardo Righetto 24 Jun '24

24 Jun '24

Dear ChimeraX team, Is there any way to install ChimeraX >= 1.8 on Linux without admin rights, like a generic Linux version that I can unpack at an arbitrary location? Our system is running Ubuntu 22.04 more specifically. Thank you! -- Ricardo Diogo Righetto

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Help_saving
by Noriega, Heather 22 Jun '24

22 Jun '24

Hello, I have a question. I created this sphere nanoparticle and have been trying to save it as a PDB (the whole sphere). But when I save "selected atoms, " I try to re-open the PDB file. It only shows the original single Span-60 that was used. Is there a way to save the copies and nanoparticles as a whole so I can minimize them altogether? I attached the session below for your reference. Thanks, Happy Friday! Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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Re: Help_saving
by Elaine Meng 21 Jun '24

21 Jun '24

Sure, if you tell me that works. I wasn't sure if #2 had all 60 or just the other 59 and it would have been another several minutes experimenting. Elaine > On Jun 21, 2024, at 1:53 PM, Tom Goddard <goddard(a)sonic.net> wrote: > > How about execute the second sym command with copies true on model #2 which has the first 60 copies? > > Tom > > >> On Jun 21, 2024, at 1:50 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Sigh, I was trying to enlist help in answering the question directly considering I've already spent hours messing around with it... especially if you think it is simple to explain. I don't think it is obvious to expect different numbers of copies just because you wanted them to be atomic instead of graphical. >> >> If she wants 3600 full atomic copies how would she do that?? >> >> Elaine >> >>> On Jun 21, 2024, at 1:35 PM, Tom Goddard <goddard(a)sonic.net> wrote: >>> >>> Hi Elaine, >>> >>> If you don't use copies true, then the first sym command changes model #1 rendering to include 60 graphical clones, and then the second sym command also on model #1 makes 60 graphical clones of the previous 60 graphical clones, so you now have 3600 graphical clones in model #1. You can see this with "info #1" which says "3600 instances". >>> >>> If you use the "copies true" option then the sym command makes a new model #2 with 60 copies. The second sym command on #1 with copies true makes 60 more copies as model #3. Of course that is a very different result then the sequence without copies true because the copies true version makes new models instead of modifying the original model. >>> >>> This all makes sense to me. >>> >>> Tom >>> >>> >>>> On Jun 21, 2024, at 1:25 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>>> >>>> Hi Tom, maybe you can figure it out?? >>>> >>>> OK I give up, I did extensive tests and can't figure it out either. I regenerated the original starting molecule (I think), attached as temp.pdb >>>> >>>> Then the overall result visible with the following, which is what she apparently wants (except with real atomic copies) although I worry it may have double copies in places, is a very packed-looking sphere: >>>> >>>> sym #1 i,2n5 center 20,20,20 >>>> sym #1 i,2n3 center 20,20,20 >>>> >>>> However if you start over with temp.pdb and then do the following, you get something much more patchy/holey >>>> >>>> sym #1 i,2n5 center 20,20,20 copies true >>>> sym #1 i,2n3 center 20,20,20 copies true >>>> >>>> I thought it might have something to do with copies replacing other copies but I tried with newModel true and still had seemingly the same issues. >>>> >>>> Maybe the more-packed appearance is actually a bug if sym w/o copies true makes more graphical copies of ones that are already graphical copies. >>>> >>>> Elaine >>>> >>>> <temp.pdb> >>>> >>>> >>>> >>>>> Begin forwarded message: >>>>> >>>>> From: "Noriega, Heather via ChimeraX-users" <chimerax-users(a)cgl.ucsf.edu> >>>>> Subject: [chimerax-users] Re: Help_saving >>>>> Date: June 21, 2024 at 12:14:50 PM PDT >>>>> To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> >>>>> Reply-To: "Noriega, Heather" <heather.noriega(a)bison.howard.edu> >>>>> >>>>> Hello, >>>>> >>>>> It is quite baffling to me why it does this. I am going to add different sessions to show you what I see. I have included each session to try and separate to explain myself and not confuse. Three of the sessions do not include the copies true command: (sym_2n3, sym_2n5, sym_both). The one with both (sym_2n3 and sym_2n5) gives me the niosome I am quite interested in with an aqueous and lipophilic compartment. I want to do a simple measure of the volume inside the large compartment, but would like to minimize the niosome as a whole first, hence needing a pdb file. However, I have done the same with the next three sessions, but adding copies true command and it is not coming up with the same result for sym_both_copiestrue. >>>>> >>>>> I hope this helps to try and understand what I am looking for, and maybe you have an answer as to why there are different results for Sym_both and Sym_both_copiestrue. >>>>> >>>>> Thank you, >>>>> >>>>> Heather Noriega >>>>> PhD-Pharmaceutical Science student >>>>> Howard University >>>>> heather.noriega(a)bison.howard.edu >>>>> 520-203-1883 >>>>> >>>>> >>>>> On Fri, Jun 21, 2024 at 2:33 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>>>> Hi Heather, >>>>> >>>>> I don't really understand why you needed two sym commands instead of one (must be something specific about your structure(s)), but whenever you want to actually save the PDB of any parts that "sym" adds you would need to include "copies true" when you add them. >>>>> >>>>> You could just do the experiment with and without it yourself and see what you get. Or save two separate PDB files, one from each command, to make sure you aren't getting duplicates of the same atoms exactly on top of each other from using sym twice. >>>>> >>>>> Elaine >>>>> >>>>>> On Jun 21, 2024, at 9:45 AM, Noriega, Heather via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>>>>> >>>>>> Hello, >>>>>> >>>>>> I do not want to save the shape of a sphere. I was using that for something else while creating the nano. >>>>>> >>>>>> Ok, that is what I did wrong. I did not include the copies true command. I have a question. I used the commands: >>>>>> >>>>>> Sym #1 i,2n3 center 20,20,20 and Sym #1 2n5 center 20,20,20 to create the sphere. Would I have to add copies true to both commands? >>>>>> >>>>>> sym#1 i,2n3 center 20,20,20 copies true >>>>>> sym#1 i,2n5 center 20,20,20 copies true >>>>>> >>>>>> And then continue with the saving process for PDB >>>>>> >>>>>> >>>>>> Thank you, >>>>>> >>>>>> Heather Noriega >>>>>> PhD-Pharmaceutical Science student >>>>>> Howard University >>>>>> heather.noriega(a)bison.howard.edu >>>>>> 520-203-1883 >>>>>> >>>>>> >>>>>> On Fri, Jun 21, 2024 at 12:37 PM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>>>>> Hi Heather, >>>>>> I can't tell what you are trying to save exactly but here are two issues: >>>>>> >>>>>> (1) when you used "sym" the Log said it was making graphical clones. (The log contents are included in the session file.) If you want full atomic copies instead of graphical clones you have to use "copies true" as explained in the help: >>>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies> >>>>>> >>>>>> (2) The big sphere seems to be a surface model, and you can't save a surface model as PDB format. Maybe you used the "shape" command, which creates surface models. But I can't tell from your message whether you are trying to save that in the file or not. >>>>>> >>>>>> I hope this helps, >>>>>> Elaine >>>>>> ----- >>>>>> Elaine C. Meng, Ph.D. >>>>>> UCSF Chimera(X) team >>>>>> Resource for Biocomputing, Visualization, and Informatics >>>>>> Department of Pharmaceutical Chemistry >>>>>> University of California, San Francisco >>>>>> >>>>>> >>>>>>> On Jun 21, 2024, at 9:16 AM, Noriega, Heather via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>>>>>> >>>>>>> Hello, >>>>>>> >>>>>>> I have a question. I created this sphere nanoparticle and have been trying to save it as a PDB (the whole sphere). But when I save "selected atoms, " I try to re-open the PDB file. It only shows the original single Span-60 that was used. Is there a way to save the copies and nanoparticles as a whole so I can minimize them altogether? >>>>>>> >>>>>>> I attached the session below for your reference. >>>>>>> >>>>>>> Thanks, Happy Friday! >>>>>>> >>>>>>> Thank you, >>>>>>> >>>>>>> Heather Noriega >>>>>>> PhD-Pharmaceutical Science student >>>>>>> Howard University >>>>>>> heather.noriega(a)bison.howard.edu >>>>>>> 520-203-1883 >>>>>>> <nano_span_60.cxs> >>>>> >>>> <sym_2n5_copiestrue.cxs> >>>> <sym_2n3_copiestrue.cxs> >>>> <sym_2n5.cxs> >>>> <sym_2n3.cxs> >>>> <sym_both.cxs> >>>> <sym_both_copiestrue.cxs> >>>>> _______________________________________________ >>>>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>>>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>>>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>>> >>> >> >> > >

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Sequence viewer colour by B factor
by isaphan＠uw.edu 21 Jun '24

21 Jun '24

How do I colour a sequence by B factor? There's an option to 'Load a sequence coloring file'. Sounds good, but how do I produce an .scf file from a structure coloured by B-factor ? There's a format explanation, but how do I get the actual data ? Grateful for any hints.

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question about coloring
by Artur Biela 21 Jun '24

21 Jun '24

dear all, I would like to color my structure (atoms) according to the LocalResolution of the map that the model is fitted in. There is a simple way to color a map according to the colors of the molecular model, but can it be done the other way around? best Artur =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Artur BIELA, PhD tel: +48-518-459-652 @: artur.biela(a)uj.edu.pl [cid:ced8e93e-4e29-47d8-b709-419b04837a3b] cryoEM faciliy manager SOLARIS National Synchrotron Radiation Centre Jagiellonian University Czerwone Maki 98, 30-392 Kraków www.synchrotron.pl<http://www.synchrotron.pl/> https://synchrotron.uj.edu.pl/en_GB/linie-badawcze/cryo-em

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Adjusting Torsion Angles
by Eleanor Streeper 20 Jun '24

20 Jun '24

Hi Chimera X, I hope you are well. I am a student at Swarthmore College and am currently trying to use Chimera X to adjust the torsion angles of glycans on a protein I have glycosylated. I tried using the same notation in your user guide, but the program says I am only entering 3 atom into the command bar. I attached images of the command and the numbering of those atoms (2nd entry in the angle/torsion measurement picture). I am trying to get the 2nd entry torsion to be 178.6 degrees. Can you let me know what I am doing wrong and how to adjust the torsion angle. Best, Ellie Streeper [image: Screenshot 2024-06-20 at 1.28.34 PM.png][image: Screenshot 2024-06-20 at 1.28.24 PM.png] [image: Screenshot 2024-06-20 at 1.35.46 PM.png]

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Re: CHimeraX and Chimera website down
by Elaine Meng 19 Jun '24

19 Jun '24

Hi Yaikhomba, Yes, we had a planned outage for server maintenance the last few days. Usually our email is out at the same time so it will not help to send email either, sorry! There was an announcement about it to this chimerax-users email list and also a news item on the ChimeraX home page, although of course you can't see the home page when the website is down. You can change the map origin with the ChimeraX "volume" command option "origin" or "originIndex", see the help for what these mean and how to use them: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dimensions> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 19, 2024, at 8:49 AM, M Y <yai25ram(a)gmail.com> wrote: > > Hi Elaine > > I hope you are well. > > I had trimmed the box size of a cryoEM-map using the RELION software (to 375 pixels from 600 pixels). To fit in a PDB model to the trimmed map, I also rescaled the trimmed map to 1.048 A/pixel from 1.07 A/pixel. However, these 2 maps do not overlay with one another (image attached). > > I wanted to change the origin of the trimmed map such that 2 maps overlay with one another. How could I do this in ChimeraX? > > I tried looking at the Chimera or the ChimeraX website. But, the website is either down or I am not able to access it (Screenshot attached). > > Your suggestions will be helpful. > > Many thanks > Yaikhomba > <image.png> > <image.png>

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Creating bond between two selected atoms
by Eleanor Streeper 17 Jun '24

17 Jun '24

Hi Chimera X, I hope you are well. I am a student at Swarthmore College and am currently trying to use Chimera X to covalently attach glycans to asparagine residues. I was able to get 3 out of 5 of the glycans attached by selecting both atoms > structure editing > build structure > adjust bonds > add reasonable bonds. I did the same process for the other 2 glycans and no bond was made. The log says bond sel, 0 bonds. The glycans are combined with the protein using the combine command. I believed it may be an issue with an unreasonable binding distance but when I moved the glycan closer, the bond still didn't work. What else should I try? Also, do you know why it is working for some glycans but not others? Best, Ellie Streeper

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Updating pdb SEQRES record with a loaded .fasta file
by Samuel Haysom 14 Jun '24

14 Jun '24

Hello, I would like to use a .fasta file that I have loaded into ChimeraX to update the SEQRES records of a PDB file that is also loaded into ChimeraX. Currently the loaded PDB file only has SEQRES records for the residues that are modelled, while the .fasta file has the full, sequence with no gaps. I have tried loading in the .fasta file and then using the $ sequence associate command to associate it with the relevant pdb chain. However, when I then save out the pdb file (using the $ save command) and then examine the pdb file it still only records the modelled residues. Is there any way to force the written pdb file to have the full sequence as uploaded in the .fasta file? I am running chimeraX version 1.7 (2023-12-19). Thanks for your help, Sam Samuel Haysom Research Scientist • Biophysics Nxera Pharma UK Limited +44 (0)1223 949201 • Steinmetz Building, Granta Park, Great Abington Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Nxera Pharma UK Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.

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RBVI downtime
by Eric Pettersen 13 Jun '24

13 Jun '24

Hi all, The RBVI compute cluster will be down for scheduled maintenance Monday and Tuesday of next week (June 17/18) which means that the Chimera and ChimeraX web sites (including the ChimeraX toolshed) and mailing lists will be down during that time. This also means that web services from Chimera/ChimeraX that access our compute cluster will not work (Blast Protein, Modeller tools, sequence realignment). We are sorry for any inconvenience. --Eric Eric Pettersen UCSF Computer Graphics Lab

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Resizing an ion model representation
by Ioannis Skalidis 13 Jun '24

13 Jun '24

Dear all, I want to show a metal ion surrounded by some side-chains for a figure panel, but the ion ball representation is quite small and gets lost in the figure panel. Is there a way to select only the specific ion and increase its size? I tried a bit with the "size" command, including the ballScale option but I had no luck. Any suggestions? Thanks a lot, Ioannis. Dr. Ioannis Skalidis | Structural Biochemist | Twitter: @imjohnskal <https://twitter.com/imjohnskal>

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Feature Request: Visual feedback on selecting menu items
by Cam McMenamie 12 Jun '24

12 Jun '24

Hello! I'm just suggesting a UI feature that I think would be very helpful. Currently, there are several menu items that do not show any feedback if they are "selected" or not, for example, in the screenshot below (hard to tell which options have been selected / toggled). This is especially the case for mutually exclusive selections such as in the 'coloring' section in the "molecule display" tab. [cid:34830b00-bed7-4734-b191-dc4fd0fad018] Thanks in advance, Cam

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Filtering PAE Contacts–Interfaces
by David S. Fay 10 Jun '24

10 Jun '24

Hi, Was attempting (unsuccessfully) to filter out lower scoring (red/yellow) PAE contacts when viewing interaction interfaces between two or more proteins. I normally use a command such as: alphafold contacts /A to /B distance 5 But then I’d like to limit what I see to regions with high pLDDT scores (blue lines). I tried playing with range, but keep getting errors. Thanks! David

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Animate RELION jobs
by James Hooker 10 Jun '24

10 Jun '24

Hi all, Is there an easy way to generate animations of RELION classification jobs in ChimeraX? I came across https://github.com/Stefan-Zukin/relionReport, but haven’t been able to get it to work. Best, James James Hooker jhooker(a)mrc-lmb.cam.ac.uk PhD candidate Löwe group, Structural Studies division MRC Lab of Molecular Biology Cambridge, United Kingdom

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Re: [Chimera-users] ChimeraX_InfoRequest
by Elaine Meng 10 Jun '24

10 Jun '24

Hello Dr. Altan Kara, Resolution is just the number of pixels width and height. To get higher resolution, specify larger numbers for the pixel width and height in the save image options (GUI or save command). Chimera has a separate setting for physical size (e.g. inches or cm) and then the pixels per physical size unit (dpi), but the result is still the total number of pixels. For example 2 inches wide with 600 pixels/inch is 1200 pixels wide. ChimeraX does not have separate settings for the physical size. For the same example, in ChimeraX you would just choose 1200 pixels wide. The result will not be marked with a physical size, however. You would have to use some other program like Photoshop if you want to mark it as 2 inches wide. If you know the physical size you want and the resolution at that size, just calculate the total pixel width and height and enter that when you save the image. For the future, if you want to ask a ChimeraX question it is better to use the ChimeraX email address: chimerax-users(a)cgl.ucsf.edu I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Jun 7, 2024, at 5:17 AM, Altan KARA (MAM-GMBE) via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > To whom it may concern, > > How we can create high resolution images with ChimeraX? > No matter what I tried still the outputted images are not in high resolution.

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ChimeraX segfaults when left on loop to make movies/images
by Artie Kushner 07 Jun '24

07 Jun '24

Hi, I hope the summer is starting off really well for you. tldr: I leave ChimeraX running movie/image generating commands from a python script in a tmux session and it segfaults on multiple machines. I was wondering if someone has encountered this before or can lend advice as to why this happens. I'd like to produce some movies (or at least pictures) in bulk (around 2000 individual molecules). I preprocess each one (load locally or open, add some representation, and either start recording a movie or "save XXXX.png"). After about 8-10 successful movies or images are produced I get a ChimeraX segfault and the process dies. This is quite perplexing to me because - I tried it on multiple machines: Ubuntu 22.04, installed from the .deb <https://www.cgl.ucsf.edu/chimerax/download.html> and Arch, installed from aur distribution. - both with `--offscreen` and `--nogui` flags and without them ( in fact, following up some threads in the mailing list it seems like it's not possible to produce movies with --nogui, just pngs) - there seems to be *no* excessive memory or page cache issues, although i haven't profiled it. Only one core is occupied when rendering both mp4/png's. Below I'm attaching a crash log from one of the machines (Ubuntu 22.04) and the description of my setup, which is a little awkward, but I don't think it's the cause since it produces some samples successfully before crashing. I hope i'm wrong. Best regards and any tips are really appreciated! I was really looking forward to having some crisp images. --------------------------------------------------------------------------------------- I start the process by calling a python script at the command line: ` chimerax --script "/home/student/dev/riboxyz/chimerax/ribrepr.py" --nogui --offscreen` when i tried generated images. This was after I gave up on getting the movies, which i did by just opening a ChimeraX gui on our workstation and calling a "loop.py" after a load the commands from "ribrepr.py" file from the gui command line. I do both in a tmux session. ```loop.py import os from chimerax.core.commands import run from concurrent.futures import ThreadPoolExecutor *DEST_DIR* = "/home/rtviii/dev/riboxyz/chimerax/movies" # This expands to ~1800 PDB ids: rcsb_id:= {4UG0, 7K00 and so on} for rcsb_id in os.listdir('/home/rtviii/dev/RIBETL_DATA'): movie_dir = os.path.join(DEST_DIR, "{}.mp4".format(rcsb_id)) print("Attempting to write ", movie_dir) if "{}.mp4".format(rcsb_id) in os.listdir(DEST_DIR): print("Skipping {}. Exists".format(rcsb_id)) continue else: run(session,"ribmovie {}".format(rcsb_id)) # <---- ribmovie command corresponds to the `*produce_and_save_movie*` in ribrepr.py below ``` The contents of the `ribrepr.py` are just to register a command for custom visualization of a given molecule + loop over molecules for image generation. ``` ribrepr.py import enum import json import os import sys from chimerax.core.commands import register, CmdDesc from chimerax.atomic import ResiduesArg, Chains, ChainArg, StructureArg from chimerax.atomic import Structure, AtomicStructure, Chain from chimerax.core.commands import run, runscript from chimerax.core.commands import CmdDesc, register, StringArg # https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/… # just a data folder, it exists. *RIBETL_DATA* = os.environ.get("RIBETL_DATA", "/home/rtviii/dev/RIBETL_DATA") class *PolymerClass*(str, enum.Enum): tRNA = "tRNA" bS1m = "bS1m" # ... another ~200 enum members, redacted for brevity CHIMERAX_COLORS = [ ["tan", "#d2b48c"], ["sienna", "#a0522d"], #... more colors redacted for brevity ] # helper function to map colors def *get_polymer_color*(polymer_class:str): polyix = list(map(lambda x: x.value, (PolymerClass))) class_index = polyix.index(polymer_class) % len(polyix) if polymer_class == None: return "gray" return CHIMERAX_COLORS[(class_index % len(CHIMERAX_COLORS))][1] def *ribosome_representation*(session, structure: AtomicStructure): for _ in list(PolymerClass): print(_.name) from chimerax.core.commands import run from chimerax.core.colors import hex_color from chimerax.atomic import Residue, Atom, Chain # i get the PDB ID from the StructureArg rcsb_id = str(structure.name).upper().split('.')[0] # <-- the structure gets opened with the basename ex "(5AFI.cif)" run(session, "set bgColor white") run(session, "sym #1 assembly 1") # take only one assembly if multiple are available run(session, "hide #2") with open(os.path.join(RIBETL_DATA, rcsb_id, "{}.json".format(rcsb_id)), "r") as f: profile = json.load(f) # load my annotations, just a json file #--------------------------------------------[ This whole bit just colors by chain annotation basically] polymers = {} polymer_chains = [ *profile["proteins"], *profile["rnas"], *profile["other_polymers"], ] [ polymers.update(x) for x in [{chain["auth_asym_id"]: chain} for chain in polymer_chains] ] c: Chain for c in structure.chains: aaid = c.chain_id polyclass = None if len(polymers[aaid]["nomenclature"]) < 1: continue else: polyclass = polymers[aaid]["nomenclature"][0] if polymers[aaid]["entity_poly_polymer_type"] == "RNA": run(session, "surf /{}".format(aaid)) run(session, "transp /{} 100".format(aaid)) run(session, "color /{} gray".format(aaid)) else: run(session, "show /{} cartoon".format(aaid, get_polymer_color(polyclass))) run(session, "color /{} {}".format(aaid, get_polymer_color(polyclass))) #--------------------------------------------[ This whole bit just colors by chain annotation basically] run(session, "graphics silhouettes true width 1") run(session, "light soft") # # ! Didn't work out for now. This is how i tried to make movies. (Loop over every structure (loop.py above) and call this command). Chimerax segfaults when looped on this. # def *produce_and_save_movie*(session, target:str): # print("GOT TARGET", target) # RCSB_ID = target # run(session, "open /home/rtviii/dev/RIBETL_DATA/{}/{}.cif".format(RCSB_ID, RCSB_ID)) # run(session, "sym #1 assembly 1") # take only one assembly if multiple are available # run(session, "ribrep #2") # run(session, "movie record") # run(session, "turn y 2 180") # run(session, "wait 180") # run(session, "movie encode /home/rtviii/dev/riboxyz/chimerax/movies/{}.mp4".format(RCSB_ID)) # run(session, "close all") # # ! This is just to not download the mmcif files i have locally. def *register_ribetl_command*(logger): def ribetl(session, rcsb_id:str): rcsb_id = rcsb_id.upper() run(session, "open /home/rtviii/dev/RIBETL_DATA/{}/{}.cif".format(rcsb_id, rcsb_id)) desc = CmdDesc( required= [("rcsb_id", StringArg)], ) register("ribetl", desc, ribetl, logger=logger) # # ! Register the above repr sequence as a command. def *register_ribrepr_command*(logger): from chimerax.core.commands import CmdDesc, register from chimerax.atomic import AtomicStructureArg, Chain, Residue, Atom desc = CmdDesc( required = [("structure", AtomicStructureArg)], required_arguments = ["structure"], synopsis = "representation ", ) register("ribrep", desc, ribosome_representation, logger=logger) *register_ribrepr_command*(session.logger) *register_ribetl_command*(session.logger) # This loop expands into a list of ~1800 PDB : 5AFI, 4UG0 and so on. for rcsb_id in os.listdir(RIBETL_DATA): run(session,"open {}".format(rcsb_id)) run(session,"ribrep #1") run(session,"save /home/student/dev/riboxyz/chimerax/{}.png width 800 height 800 transparentBackgroun d true".format(rcsb_id)) run(session,"close all") ``` Let me know if i can elucidate this situation further with hardware specs or whatnot. I'm quite at loss as to how to proceed with this.

2 2

Alpha fold not responding
by Cao,JingJing 07 Jun '24

07 Jun '24

Hello, I was using the program to run Alphafold prediction, it’s keep giving me error messages (502): The server encountered a temporary error and could not complete your request. Please try again in 30 seconds. That’s all we know. How to solve this problem? Thanks, JingJing The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

2 1

Modifying the transparency of a specific region within a single map
by 张楠 07 Jun '24

07 Jun '24

Dear developers, How can I change the transparency of a specific region within a single map, similar to what is shown in the attached image? Is this possible to do in ChimeraX?" Looking forward to your answer, thank you！ Best regards, Nan zhangnan(a)nankai.edu.cn

3 2

Renaming of "Non-standard residues" upon file opening
by Mikkel Dahl Andreasen 07 Jun '24

07 Jun '24

Hello I have a question regarding ChimeraX renaming residues upon loading pdb files. I am specifically referring to a pdb file containing the following lines: TITLE PLACEHOLDER_TITLE REMARK PLACEHOLDER_REMARK CRYST1 100.000 100.000 100.000 90.00 90.00 90.00 P 1 1 MODEL 1 ATOM 1 NC3 DOPCA 1 93.725 50.146 69.265 1.00 0.00 ATOM 2 PO4 DOPCA 1 93.471 50.284 66.361 1.00 0.00 ATOM 3 GL1 DOPCA 1 93.591 50.038 63.469 1.00 0.00 ATOM 4 GL2 DOPCA 1 94.818 50.396 63.498 1.00 0.00 ATOM 5 C1A DOPCA 1 93.669 50.374 60.367 1.00 0.00 ATOM 6 D2A DOPCA 1 93.738 49.939 57.365 1.00 0.00 ATOM 7 C3A DOPCA 1 93.390 49.936 54.359 1.00 0.00 ATOM 8 C4A DOPCA 1 93.358 50.194 51.480 1.00 0.00 ATOM 9 C1B DOPCA 1 96.261 50.393 60.395 1.00 0.00 ATOM 10 D2B DOPCA 1 96.060 50.114 57.261 1.00 0.00 ATOM 11 C3B DOPCA 1 96.224 50.032 54.669 1.00 0.00 ATOM 12 C4B DOPCA 1 95.844 50.135 51.528 1.00 0.00 TER END When I load this file into ChimeraX using "open file.pdb" it renames the residue name "DOPC" to "DOP". A table appears in the Log regarding "Non-standard residues in file.pdb" wherein it lists "DOP - (DOP)" without mentioning "DOPC". However, when I open another file which contains many different types of molecules, then it does not rename "DOPC" to "DOP", even though the "Non-standard residues in file.pdb" table also appears, though this time with an entry containing "DOPC - (DOPC)". I have also previously experienced that ChimeraX renames some (not all) of my cholesterol molecules to "CHO" (instead of using the actual residue name which is "CHOL"). I had a look through the documentation for the "open" command, but I couldn't find anything useful about it. I was wondering why this is happening and if there is a way to prevent it. And just so i am clear, by prevent I don't mean revert (e.g. rename them back to "DOPC" after loading), but actually preventing the initial renaming done by ChimeraX. Kind regards, Mikkel Dahl Andreasen

3 3

modeller fails in chimerax RC-1.8
by Roberto Marabini 07 Jun '24

07 Jun '24

Hi, I just installed chimerax RC-1.8 and tried to use "modeller" (tools->sequence->modeller comparative). The resulting error message is attached to this email. If I use chimerax 1.7 with the very same data modeller works. Am I doing something wrong or did I find a bug? cheers Roberto Follows the complete log: === modeller comparative aligned_1.fasta:2 numModels 5 fast false multichain false hetPreserve true hydrogens false waterPreserve falseWebservices job id: GN1G33GHX39IPCAE Modeller job (ID GN1G33GHX39IPCAE) finished Modeller error output Traceback (most recent call last): File "ModellerModelling.py", line 74, in <module> a.make() File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py", line 141, in make self.homcsr(exit_stage) File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py", line 624, in homcsr self.check_alignment(aln) File "/usr/lib64/python3.8/site-packages/modeller/automodel/automodel.py", line 577, in check_alignment aln.check() File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 213, in check self.check_structure_structure(io=io) File "/usr/lib64/python3.8/site-packages/modeller/alignment.py", line 222, in check_structure_structure return f(self.modpt, io.modpt, self.env.libs.modpt, eqvdst) _modeller.SequenceMismatchError: read_te_291E> Sequence difference between alignment and pdb : Modeller run output MODELLER 10.5, 2024/01/19, r12711 PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS Copyright(c) 1989-2024 Andrej Sali All Rights Reserved Written by A. Sali with help from B. Webb, M.S. Madhusudhan, M-Y. Shen, G.Q. Dong, M.A. Marti-Renom, N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser, R. Sanchez, B. Yerkovich, A. Badretdinov, F. Melo, J.P. Overington, E. Feyfant University of California, San Francisco, USA Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK Kind, OS, HostName, Kernel, Processor: 4, Linux wilkins.cgl.ucsf.edu 4.18.0-513.24.1.el8_9.x86_64 x86_64 Date and time of compilation : 2024/01/20 00:40:16 MODELLER executable type : x86_64-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2024/06/06 03:33:20 environ____W> The class 'environ' is deprecated; use 'Environ' instead openf___224_> Open $(LIB)/restyp.lib openf___224_> Open ${MODINSTALL10v5}/modlib/resgrp.lib rdresgr_266_> Number of residue groups: 2 openf___224_> Open ${MODINSTALL10v5}/modlib/sstruc.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 191566 187.076 0.183 Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 192094 187.592 0.183 openf___224_> Open ${MODINSTALL10v5}/modlib/resdih.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 240694 235.053 0.230 rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf___224_> Open ${MODINSTALL10v5}/modlib/radii.lib Dynamically allocated memory at amaxlibraries [B,KiB,MiB]: 253994 248.041 0.242 openf___224_> Open ${MODINSTALL10v5}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf___224_> Open ${MODINSTALL10v5}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf___224_> Open ${MODINSTALL10v5}/modlib/mnch1.lib openf___224_> Open ${MODINSTALL10v5}/modlib/mnch2.lib openf___224_> Open ${MODINSTALL10v5}/modlib/mnch3.lib openf___224_> Open ${MODINSTALL10v5}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 automodel__W> The class 'automodel' is deprecated; use 'AutoModel' instead openf___224_> Open alignment.ali Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 282425 275.806 0.269 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 297517 290.544 0.284 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 312917 305.583 0.298 Dynamically allocated memory at amaxalignment [B,KiB,MiB]: 343717 335.661 0.328 Dynamically allocated memory at amaxsequence [B,KiB,MiB]: 344285 336.216 0.328 read_te_291E> Sequence difference between alignment and pdb : x (mismatch at alignment position 1) Alignment XSLSDKDKAAVRALWSKIGKSADAIGNDALSRMIVVYPQTKTYFSHWPDVTPGSP PDB SLSDKDKAAVRALWSKIGKSADAIGNDALSRMIVVYPQTKTYFSHWPDVTPGSPH Match * * Alignment residue type 24 (X, UNK) does not match pdb residue type 16 (S, SER), for align code 1pbx.cif_2/A (atom file 1pbx.cif_2), pdb residue number " 1", chain "A" Please check your alignment file header to be sure you correctly specified the starting and ending residue numbers and chains. The alignment sequence must match that from the atom file exactly. Another possibility is that some residues in the atom file are missing, perhaps because they could not be resolved experimentally. (Note that Modeller reads only the ATOM and HETATM records in PDB, NOT the SEQRES records.) In this case, simply replace the section of your alignment corresponding to these missing residues with gaps. read_te_288W> Protein not accepted: 1 1pbx.cif_2/A No output models from Modeller; see log for Modeller text output.

3 3

Converting a carbonyl group to carboxylic acid group
by Prathvi Singh 06 Jun '24

06 Jun '24

Hi Elaine, I have a SER residue which is in the middle of a polypeptide chain. Is there a way in chimera/chimeraX to specifically extract this residue such that the carbonyl group bonded to its N-terminal NH group also gets extracted but is converted to carboxylic acid group (-COOH group) before extracting? Thanks in advance, Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

2 4

Molecule_to_sphere
by Noriega, Heather 06 Jun '24

06 Jun '24

Hello, I hope this email finds you well. I have a molecule that I created through the build feature in Chimera, and what I would like to do is just create a sphere of as many copies as it can fit to see the estimated encapsulation volume. However, there is no symmetry assembly to use the matchmaker and I was trying to use the sym command, but it isn't even recognizing the command. sym #1 i,222 sym #1 i, n25 Sym#1 i, 222r I have tried others with the center command, and I also tried to add copies false NewModel true at the end. What am I plugging in wrong? The molecule is saved as a pdb, and uploads no issue on ChimeraX. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

2 4

Push and pulling model/map towards/away
by Pranav Shah 05 Jun '24

05 Jun '24

Hi Team, Chimera used to have a really nice feature that allowed for a model to be pushed away or pulled towards the user. How do I access this feature in ChimeraX? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

3 8

Selecting the N or C-terminus of every chain in a PDB file
by André Graça 05 Jun '24

05 Jun '24

Hi everyone! I could not figure this one out just yet, but it might be easy (?): I am interested to make a quick selection that targets the first or last atom of all the chains present in a given PDB file. /André Graça

2 1

Fetch many pdbs/maps from the pdb-redo?
by Francisco Murphy Pérez 05 Jun '24

05 Jun '24

Dear all I thought this was going to work, `open "1iee, 2blx, 2bly" fromDatabase redo format mmcif`... but it does not. I have many more ids that I want to open... Can I fetch them all with a single command? Thanks

2 2

Morph command for protein-ligand complexes
by Enrico Martinez 05 Jun '24

05 Jun '24

Dear ChimeraX users! I have a question about recording movie with the transitions between different conformations using morph command. Having five conformations for the same protein, after its supermpostiion using mm #2-5 to #1 I generated a trajectory with the transition using: morph #2,3,4,5,6 core 0.1 frames 100 wrap f rate linear And then recorded movie using: # start recording movie record size 3840,2160 supersample 1 coordset #7 1,400,1 computeSs true wait 400 My question is about morph command. Assuming that all 5 models are very well superimposed and the difference is only the bound ligand (which is different in every model!), would it be possible to include these different ligands in the final morphed trajectory, thus making a smooth transition between different binding poses ? Many thanks in advance ! Enrico

2 2

How to reproduce the output of "info" in python script?
by Artie Kushner 04 Jun '24

04 Jun '24

Hi there, hope you are all doing well I'm wondering if anyone has a good idea of how to reproduce the output of the *info* command in the GUI inside a python script. Precisely the *info* command without any specifiers s.t. that all models and submodels are listed with minimal info. Like the following: *...#1.87, 4v6x Cu, shown419 atoms, 421 bonds, 56 residues, 1 chains (Cu)#1.88, 4v6x Cv, shown419 atoms, 421 bonds, 56 residues, 1 chains (Cv)#1.89, 4v6x Cz, shown1741 atoms, 1769 bonds, 217 residues, 1 chains (Cz)* Perhaps there is a better way to do this, but my use case is splitting a bigger structure into multiple chains (as you can tell from above there are 89 chains in 4V6X). I'd like to be able to correlate chain IDs (ex. *Cz*) with the model identifiers (ex. *#1.89*) programmatically from within python to script against individual chains further. I'm sure there is more than one way to do it, but i haven't been able to find either so far. Most that i found is the model_info command: *from chimerax.list_info.util import spec, model_info...def test_func(session, structure: AtomicStructure): print(model_info(structure))**<<<Missing or invalid "structure" argument: must specify 1 atomic structure, got 89 for "#1".* *def register_ribrepr_command(logger): from chimerax.core.commands import CmdDesc, register from chimerax.atomic import AtomicStructureArg, Chain, Residue, Atom desc = CmdDesc( required = [("structure", AtomicStructureArg)], required_arguments = ["structure"], synopsis = "representation ", ) register("test_func", desc, test_func, logger=logger)* but it presupposes that I pass the model by spec I pass the "top-level" structure. It throws error saying that it contains 89 instead of 1 structures: *Missing or invalid "structure" argument: must specify 1 atomic structure, got 89 for "#1".* Any other way of getting at the correspondence dict between chains/"submodels" created with i.e. *`split chains`* and their chain_id's (aka *auth_asym_id* 's) in Python space would work for me. Perhaps there is a way to list all objects in the "Models" section (picture below)? Thanks in advance Artie [image: image.png]

2 2

Question/ GPCR complex
by Ranti Dev Shukla 03 Jun '24

03 Jun '24

Hello, Greetings from NIH, Maryland. I am trying to make FRET for G-proteins. I put CFP protein within G.alfa2 on a loop between two nearby helixes and YFP protein on the N-terminal of G-beta. I made the complex using Alphafold but how to see this complex along with the membrane? Is there some command for it please? I would appreciate your kind help. Thanks Ranti Best wishes, Ranti Dev Shukla Visiting Fellow, NIH, Rockville, MD Email: rantibio2(a)gmail.com *rantibio3(a)gmail.com <rantibio3(a)gmail.com>* Phone: +1 865-910-2985 *Teachers* make a lasting impact in the lives of their students

2 1

Rotation of the multi-model object using the symmetric axis
by Enrico Martinez 03 Jun '24

03 Jun '24

Dear Chimera-X users! I am dealing with the visualisation of a complex dimer where each monomer is defined as a separate model like #1 and #2. For visualisation purposes I need to rotate the input construct by 180 degrees with the axis of rotation in the middle between the two monomers to avoid the shift of the complex in the x-plane at the end. That's what I have tried: # turn on 180 deg during 10 sec roll y 0.72 250 center #1,2 protein wait 250 but the construct still shifted a bit towards one of the monomers. How could I do ii using the rotation axis, which would be in the center between them ? Many thanks in advance Enrico

3 4

Conversion of multiple files into PDB
by Enrico Martinez 03 Jun '24

03 Jun '24

Dear ChimeraX Users ! I am dealing with the analysis of multiple structural coordinates generated by AlphaFold for a target protein in *.cif extension. My goal is superimpose all the coordinates to the first model and save them in .pdb as separate files. So my script could be: open ./*.cif match #2-6 to #1 # probably there is a better solution # and some command for save What could be the solution to save all the coordinates in automatic way in separate pdb with the name patterns corresponded to the ID of these models ? Many thanks in advance Enrico

3 3

attributes from viewdockx.
by Krishnan Raman 31 May '24

31 May '24

Hi guys, * Make ViewDockX table information available as model attributes<https://rbvi.github.io/chimerax-recipes/vdx_attrs/vdx_attrs.html>. December 17, 2021 Used this Py to register my attributes into chimerax. Is there a way to display the attributes next to the model of the ligand? Thanks Krish Krishnan Raman Executive Director, Structural Biology BioCryst Pharmaceuticals CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

2 5

Grid mode for multiple superimposed models
by Enrico Martinez 31 May '24

31 May '24

Dear ChimeraX users ! I am working on the structural analysis of the predictions of the alpha fold loaded in Chimera as different models. Do we have an option that would allow us to take each model as an element of the grid so that the superimposed models could be displayed side by side (e.g. in one row for 1-3 models or in 2 rows for 4-6 models etc)? I've seen this option in P*mol, but would like to try it in ChimeraX if it exists! Many thanks in advance Enrico

2 2

ChimeraX question
by Meden Isaac-Lam 30 May '24

30 May '24

Hello UCSF Chimera Team, I used Chimera and AutoDock Vina about 2 years ago. I just downloaded ChimeraX and I am trying to learn it. However, I forgot how to link AutoDock Vina. In the previous Chimera, it was under Tools and Surface Binding Analysis. Any suggestion on how to do it? Thanks. Your assistance is greatly appreciated. Sincerely, Meden F. Isaac-Lam Purdue University Northwest

2 2

Error installing bundle: No module named pandas
by Ricardo Righetto 29 May '24

29 May '24

Hi, Not sure if this should be reported here or to the bundle developers directly, but in any case here it goes: When trying to install the ArtiaX plugin on ChimeraX v1.7.1 on Ubuntu 22.04 from the toolshed (both via command line and through the GUI) I ran into the following error: *** error: subprocess-exited-with-error × python setup.py egg*info did not run successfully. │ exit code: 1 ╰─> [10 lines of output] Traceback (most recent call last): File "", line 2, in File "", line 34, in File "/tmp/pip-install-ni7khioh/starfileddcd2480b29b4cad9233c413b6568ba0/setup.py", line 2, in from starfile.version import VERSION File "/tmp/pip-install-ni7khioh/starfile_ddcd2480b29b4cad9233c413b6568ba0/starfile/__init* .py", line 1, in from .functions import open, read, new, write, version, star2excel File "/tmp/pip-install-ni7khioh/starfile _ddcd2480b29b4cad9233c413b6568ba0/starfile/functions.py", line 3, in import pandas as pd ModuleNotFoundError: No module named 'pandas' [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed × Encountered error while generating package metadata. ╰─> See above for output. note: This is an issue with the package mentioned above, not pip. hint: See above for details . *** That is, it was complaining that the pandas package was missing when trying to install the starfile package, which in turn is a dependency of ArtiaX. I'm puzzled why it wasn't able to install pandas by itself, since it is listed as a dependency of starfile. Anyway, after trying many different things, I found out that I could install pandas via pip directly through the ChimeraX command line interface: pip install pandas And after that the bundle installation worked just fine. Not sure what to make of this, but maybe it's useful to developers or other users running into the same issue. Thank you, -- Ricardo Diogo Righetto

1 0

Question Regarding rangecolor kdHydrophobic command
by Knotts, Garrett 29 May '24

29 May '24

Good morning, I am in the process of switching over from Chimera to ChimeraX. I have found ChimeraX to be incredibly more user friendly and well-designed. I wanted to reach out regarding the rangecolor kdHydrophobic command. I often use this command in chimera to color protein surfaces based on hydrophobic character. However, we have a color scheme which our lab has consistently used. In the switch from Chimera to ChimeraX, I have not found a way to color by hydrophobicity with our color scheme using this or other commands, but I have found a way to color hydrophobic regions onto surfaces, without the ability to change the colors. Is there a way to do this in ChimeraX? Thanks for the help! Best, _______________________________ Garrett Knotts Undergraduate Lab Assistant (Johnson Lab) Legislative Director of the Mississippi State University Student Association Vice President of Honors Ambassadors Sigma Phi Epsilon Learning Community Coordinator [cid:8783bc97-b3f7-4f42-85c5-130c16ad956f]

2 1

Behavior of "cd" when executed through a script
by Vorländer,Matthias Kopano 29 May '24

29 May '24

Dear ChimeraX team, I have a series of scripts that contain a “cd” statement to set the working directory. I execute the scripts (which opens a model and map and colors the map). I then manually adjust the orientation and threshold and want to save a picture with “save map.png” (I want this png tp be saved in the folder that I set with the script). I have noticed that in this scenario ChimeraX has “forgotten” the cd statement from the script file and has fallen back to default working directory (or the last working directory manually set in the session before I exectuted my script). At least for me it would be more convenient and logical if the working directory can be set and maintained after habing executed a script. Note: if I don’t execute the script by double clicking but by copy/paste, the working directory is correctly maintained. Would be great if the behavior could be adjusted 😊 Many thanks and best wishes, Matthias

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Command not found from cxc file v1.7.1 on M2 Mac
by Hong Glenn Meng ZHAN 29 May '24

29 May '24

Evening all, I was trying to color code my imod models based on their volume (see attached). It worked ok for me just one model file opened in ChimeraX. When I was doing anther model file, I can passed the individual command in the command line to change color: color #1.1 #ceecc8 However, when I generate a cxc file and open it from command line or click on Open, it showed Unknown command: color #1.1 #ceecc8 Any input where I was not doing correctly? Thanks for helping! -Hong [Screenshot 2024-05-28 at 11.22.11 PM.png][image2.png]

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Python scripting for Dipole moment calculation
by andreumormaldon＠outlook.com 28 May '24

28 May '24

Hi all! I am trying to calculate the dipole moment of different proteins at different pH values. The .pdb and .dx files are generated with pdb2pqr and apbs software. I have found a script that is written for chimera, but it seems that the modules are not translated to ChimeraX, or at least I am not able to make it work. So I have decided to try to write my own script. So far I am able to obtain the center of mass of the protein as well as the charges of all the atoms in the molecule, but I cannot find a way to build a vector to where calculate the dipole (as it is done in the chimera script). Can anyone give me some insights? Does ChimeraX have as well the class Vector and Point? Thank you very much for your help! Best, Andreu

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Is it possible to set attribute on chain via Python script?
by Artie Kushner 28 May '24

28 May '24

I apologize in advance if this is off topic. I heard that people use chimerax mailing list to share tips and ask for help and saw some archives online that came in handy. I'm wondering if it's possible to set an attribute on the whole atomic chain (for future byattribute coloring) the way it is done in the example with Atom/Residue ? ( https://rbvi.github.io/chimerax-recipes/helixmlp/helixmlp.html) I'm trying something similar in my script: ``` from chimerax.core.commands import run from chimerax.atomic import Residue, Atom, Chain # the regular Cmd setup.. c:Chain polyclass:str = ... input from external spruce c.polymer_class = polyclass Chain.register_attr(session, 'polymer_class', 'Polymer Class', attr_type = str) ``` But when i run `color byattribute polymer_class /6 palette lipophilicity` it's not getting picked up: `No known/registered numeric attribute polymer_class`. Maybe it's not possible to color by string attributes? Thanks a lot for your advice Artem

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Morph Trajectory to smooth motion
by Alexander Hung Lee 26 May '24

26 May '24

I've morphed between a series of models/submodels to create a smooth trajectory but is it possible to morph a loaded trajectory that's topology and trajectory file (.nc)? Or is there another way to smooth the motion of it if morph is just to create a trajectory between models? 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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Surface caps not drawn in script
by Daniel Asarnow 25 May '24

25 May '24

Hi Tom/Elaine, I have a series of models with SES surfaces and per-model clipping, and I am trying to create figures for each in a script with several blocks like the following: hide target m show #1 target ms save fig1.png If I run the commands myself, the figures are as expected, but when I run the script / copy and paste several of these blocks, the surface caps aren't drawn. Am I missing something? Or can I trigger the caps somehow? Thanks! Best, -da

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Re: Reg. alphafold contacts maxPae parsing
by Greg Couch 24 May '24

24 May '24

HI Anthony, Please send all ChimeraX question to the chimerax-users mailing list, so the appropriate person can answer you. While in general I am not involved with the alphafold support, in this particular case, I believe the answer is to use the current ChimeraX release candidate or daily build. Alphafold 3 changed the PAE format, so new code had to be written. And that has been mentioned on the mailing list, so if you are not already a member, I recommend joining. -- Greg On 5/24/2024 6:24 AM, Antony Merlin Jose wrote: > Dear Greg, > I have been using the alphafold contacts to parse the .pkl files to > show the pseudobonds in ChimeraX (e.g., alphafold contacts #1/A to > #1/B maxPae 5 distance 6). The .pkl files were generated from a > locally installed Alphafold 2.3. Now that there is an AlphaFold 3 > server, (https://golgi.sandbox.google.com/) I ran some complexes on > there and downloaded the results. The results include .json files that > have the PAE information. Would using the same commands with this file > also result in the correct parsing of the PAE values? How can I see > the python code that corresponds to each command on ChimeraX? > Thank you > Best, > Antony >

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Zn fingers
by Dyda, Frederick (NIH/NIDDK) [E] 24 May '24

24 May '24

I have a structure with some Zn fingers. How can I describe the Zn2+ tetrahedral environment for Isolde? Cryo EM density is less than spectacular... Thanks. Fred ******************************************************************************* Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular Biology Fax: 301-496-0201 NIDDK Bldg. 5. Room 338 e-mail: Fred.Dyda(a)nih.gov Bethesda, MD 20892-0560 URGENT message: 2022476710(a)msg.fi.google.com Google map: 39.001168, -77.102048 http://www-mslmb.niddk.nih.gov/dyda/dydalab.html *******************************************************************************

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Fwd: some more clarifications on this?
by Eric Pettersen 23 May '24

23 May '24

> Begin forwarded message: > > From: Krishnan Raman <RKrishnan(a)BIOCRYST.com> > Subject: some more clarifications on this? > Date: May 23, 2024 at 8:22:08 AM PDT > To: "chimerax-users-owner(a)cgl.ucsf.edu" <chimerax-users-owner(a)cgl.ucsf.edu> > > Aligning two VR headsets in one room. Two Vive or Vive Pro VR headsets can be used in the same room, each connected to its own computer. Each headset uses the same pair of base stations. A problem sometimes arises that the two headsets do not see the ChimeraX structures displayed at the same location in the room. Specifically, one headset may see the structure positions as if the room is rotated 180° relative to the other headset. This happens because the SteamVR room setup is run separately on each computer and produces a different coordinate system. For structures to have the same room position in both headsets, the room boundaries traced using SteamVR room setup should be the same for both computers. The first step of SteamVR room setup in which users are asked to point the hand controller at the screen and click is the key to avoiding 180° misorientation. At that step, it is important to point along the short axis of the rectangle defining the room bounds (that will be traced in a later step). SteamVR chooses between two coordinate system orientations rotated 180° from each other based on the direction of pointing. If pointing is along the long axis of the rectangle bounds, a slight tilt toward the left or right of the long axis produces opposite coordinate system orientations. Pointing along the short axis instead is a reliable way to make both computers use the same orientation. (The computer screen position is irrelevant.) > > https://www.cgl.ucsf.edu/chimerax/docs/user/commands/meeting.html#:~:text=T… <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/meeting.html#:~:text=T…>. > > I was successful in doing a hybrid meeting with one 2d monitor and one VR headset (quest pro) -air linked. I do see that my images in the VR are rotated by 180 deg. With respect to the 2d monitor. Do I still have to run steam vr on both computers to bring them into same coordinate system? > > > > Krishnan Raman > Executive Director, Structural Biology > BioCryst Pharmaceuticals > > > > > CONFIDENTIALITY NOTICE > > This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you. >

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Re: Replies from mailing list not send to inbox
by Alexander Hung Lee 23 May '24

23 May '24

In reply to Elaine Meng, I went to this link but it already confirmed "Member already subscribed." I also didn't get a direct email from you even though you included my individual email address. Currently replying by going to the mail archive and clicking the reply button in the thread. https://mail.cgl.ucsf.edu/mailman/mailman3/lists/chimerax-users.cgl.ucsf.ed… 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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Re: Match atoms
by Alexander Hung Lee 23 May '24

23 May '24

Thanks Elaine! 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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Replies from mailing list not send to inbox
by Alexander Hung Lee 23 May '24

23 May '24

Hi everyone, Earlier I had sent a help request "Match Atoms." After looking in the online mail archive, I found that I received replies to my problem, but didn't get an email. How do I fix this? I accidentally sent the email again thinking it wasn't received... Sorry, 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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Match atoms
by Alexander Hung Lee 23 May '24

23 May '24

Hi everyone, I'm trying to use the match command (not matchmaker) to align the ring atoms of a ligand. The command gives "No matrix compatible with both reference structure and all match structure" and translates the match command to matchmaker in the reply log. However, in Chimera I'm able to align jjst those ring atoms with the match command. Of course, using matchmaker on just those atoms in Chimera gives "No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix" tl;dr. Trying to align ring atoms of a ligand instead of protein chain Chimerax mask 1 = #1:203@C19,C20,C21,C16,C17,O18 mask 2 = #2:125@C2,C3,C4,C5,C6,O6 matchmaker: No matrix compatible with both reference structure and all match structures match: Same as above. In reply log, match is extended to matchmaker Chimera mask 1 = #0:203@C19,C20,C21,C16,C17,O18 mask 2 = #1:125@C2,C3,C4,C5,C6,O6 matchmaker: No chains in reference structure #1 compatible with BLOSUM-62 similarity matrix match: Gives me RMSD ** I need this atom match functionality in ChimeraX 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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Fwd: Uncaught bounce notification
by Eric Pettersen 22 May '24

22 May '24

> Begin forwarded message: > From: Allen Place <place(a)umces.edu> > Subject: Re: Your message to chimerax-users(a)cgl.ucsf.edu awaits moderator approval > Date: May 16, 2024 at 5:11:31 AM PDT > To: chimerax-users-bounces(a)cgl.ucsf.edu > > > Help with commands. I know how to Select regions in my protein sequence, but How do I select different colors for those selections? These are various modules that I have assigned prior to the prediction based on homology. > Al > > >> On May 15, 2024, at 9:45 AM, chimerax-users-bounces(a)cgl.ucsf.edu wrote: >> >> Your mail to 'chimerax-users(a)cgl.ucsf.edu' with the subject >> >> Alphafold3 models >> >> Is being held until the list moderator can review it for approval. >> >> The message is being held because: >> >> The message is not from a list member >> >> Either the message will get posted to the list, or you will receive >> notification of the moderator's decision. > > Allen R. Place(he/him/his) > Professor, Associate Director of Research, > Director of BASLab, Director of HAB-CTI > Institute of Marine and Environmental Technology > University of Maryland Center for Environmental Sciences > The Rita Rossi Colwell Center > 701 East Pratt Street > Baltimore, MD 21202 > 410-234-8828 > place(a)umces.edu > > ALAN, ALLAN, ALLEN > From the Gaelic word for “cheerful” > > He is smart, makes friends easily, and never loses his sense of humour. > > He thrives on a challenge > > > Sign up to receive our quarterly newsletter, Inside IMET! > > >

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Improvement suggestion
by Lionel Carlo Clarens 22 May '24

22 May '24

Dear User List, I am a frequent user of ChimeraX. Currently, the only way to create animations is via the command line. In contrast, the older Chimera version has an intuitive, user-friendly interface for making simple and effective animations. It would be an excellent and straightforward improvement to migrate this functionality from Chimera to ChimeraX, as I currently need to use both software. Best regards, Lionel C.

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question about using ChimeraX
by 天剑流痕 21 May '24

21 May '24

This chimerax software is very useful. Could you please tell me how to connect two amino acid residues or atoms in the protein 3d diagram 天剑流痕 475514296(a)qq.com  

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Sign up for the user group's email list
by Md Saiful Islam - MRC LMB 20 May '24

20 May '24

Hi Is it possible please to add me to the Chimera X user group's email list. Cheers Saif

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Doubt
by GOTZONE BARANDIKA 19 May '24

19 May '24

Dear developers, I am a new user of ChimeraX. I need to create dimers in order to analyse adsorbate-adsorbant interactions for DFT calculation. I am able to create the image on the screen, but I don´t know how to save the atomic coordinates of the dimer in a single file. If I save a .pdb file in order to produce a .xyz file, just the information of one of the entities is kept. Can you please help me? [cid:image003.jpg@01DAA921.4F8EE270] Best regards, [Diapositiva1]

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How to copy fitted monomer in a symmetric map?
by Noha Elhosseiny 18 May '24

18 May '24

Hi, I have a map with C15 symmetry in which I already refined the fitting of a single monomer (asymmetric unit) in the map using coot. I now want to generate the complete 15-mer atomic model. I watched your tutorial : ( https://youtu.be/v3jI43YJQMg?si=WeQg2ef2MPOw2J7H) and I tried to use the command "sym #2 (my model) C15 to do that, but instead of getting the monomers fitted around the axis of symmetry, I could see that 15 versions were visible but in a circular circumference around my map, away from the center, and the monomers are widely spaced from one another. I kind of expected this because I did not specify any coordinates to do this copying, so how can I fix this? Another question: when I use the command "measure symmetry" I get "C3, center 270 270 244". So I do not understand why it's detecting a C3 when it's clearly a C15. I think the above coordinates of the center can be used to solve my fitting problem but I am not exactly sure how. Finally I understood that even if the monomers appear properly fitted, given I manage to do it, that these are just graphical copies. So how can I then make real copies of the graphical representation of the 15-mer? Thanks Noha -- *Noha M. Elhosseiny, PhD* Department of Microbiology & Immunology Faculty of Pharmacy, Cairo University. Kasr El-Ainy St, Cairo, Egypt, 11562- Lab C-407 Website: https://eg.linkedin.com/in/nohaelhosseiny <https://eg.linkedin.com/in/nohaelhosseiny>

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Re: Displaying surface model of blob clostest to a centroid
by Tom Goddard 18 May '24

18 May '24

Hi Yoseph, So you have a volume and you have markers shown in ChimeraX and you wanted to show only the connected surface piece from the volume contour surface that is closest to a specific marker? Do I have that right? You show in your image a lot of markers, but you only want to find the surface piece close to one of them? And you just want to show it and hide all the other parts of the surface? What if the closest surface piece is far away? Or what if a tiny spec of surface is close, but a bigger surface piece is nearby? I think that would require writing some Python code. There is nothing in ChimeraX that I can think of that computes connected surface pieces that are close to a marker. Did you consider just showing a zone of the surface around the marker out to a certain specified distance? The ChimeraX surface zone command does that, described here https://www.cgl.ucsf.edu/chimerax/docs/user/commands/surface.html#zone Tom > On May 17, 2024, at 4:05 PM, Yoseph Loyd <yoseph.loyd(a)mines.sdsmt.edu> wrote: > > Hi Tom, > > Sorry I was having a difficult time uploading an example image to the form. I'll attach it below, I'm displaying tracked centroids as small spheres. I was hoping that there existed a way to display the nearest yellow blob to the tracks I care about. The yellow blobs signal wise are full binary objects. Thank you for helping me with this. > > Best, > Yoseph > > On Fri, May 17, 2024 at 4:43 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Yoseph, >> >> I don't know what you mean "objects that fit to a centroid that I've tracked". What kind of object? The centroid of what? And why isn't it displayed currently? You'll have to explain better. >> >> Tom >> >> > On May 17, 2024, at 2:07 PM, Yoseph Loyd via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> > >> > Hi, >> > >> > My name is Yoseph, I was wondering if there is a way to display objects that fit to a centroid that I've tracked and imported into chimera. Thank you for taking the time to read this and have a nice day. >> > >> > >> > Best, >> > Yoseph >> > _______________________________________________ >> > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >> > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >> > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >> > >>

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Displaying surface model of blob clostest to a centroid
by yoseph.loyd＠mines.sdsmt.edu 17 May '24

17 May '24

Hi, My name is Yoseph, I was wondering if there is a way to display objects that fit to a centroid that I've tracked and imported into chimera. Thank you for taking the time to read this and have a nice day. Best, Yoseph

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Re: [Chimera-users] Saving symmetry model in pdb format
by Elaine Meng 17 May '24

17 May '24

Hi Kailash Singh Bisht, You sent the message to chimera-users which is for Chimera questions. However, you said "ChimeraX team" so I am guessing that you are actually using ChimeraX, and I CC'd the chimerax-users address above -- please use that one for ChimeraX questions. You didn't say how you created the symmetry structure. I am guessing that when you create the symmetry structure with the "sym" command, you need to include the option "copies true" so that you get real atomic copies instead of just graphical clones. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On May 17, 2024, at 12:27 AM, Kailash Singh Bisht via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello ChimeraX team > > I am trying to export the symmetry structure of the protomer virus protein as a pdb file but whenever I am saving that model it only saves the same protomer instead of the whole symmetry structure. Can you please help? How to export those symmetry models as PDB files > > -- > With Regards > Thanking You > > Kailash Singh Bisht > Ph.D. Student

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prediction of 5mC modification and transcription factor interaction through AlphaFold 3
by Kaan Okay - HI 17 May '24

17 May '24

Hi, I use Alphafold through UCSF ChimeraX. It is a very nice tool, I believe its developers have done a good job. As you know, AlphaFold 3 is a new model that allows us to predict DNA modification and protein interactions (https://www.nature.com/articles/s41586-024-07487-w) What I wonder is when this model will be transferred to UCSF ChimeraX and whether we can predict protein interactions and DNA modifications (e.g., 5mC modification on cytosine bases in DNA). I'm looking forward to hearing from you. All the best.

2 1

Cinematographic effects in MD movie recording
by Enrico Martinez 17 May '24

17 May '24

Dear Chimera-X users ! I would like to add some cinematographic effects such as changing the camera angle back and forth during a short recording time of MD movies. Could you suggest some scripting tricks that I could add to the following coordset routine: # start recording movie record size 3840,2160 supersample 1 ## play movie from beginning to the end coordset #1 1,1000,1 wait 1000 etc Would it be possible to bend the camera automatically e.g. during the first 250 steps of recording ? Any other possibilities ? Yours with thanks Enrico

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Displaying angles in chimera
by Prathvi Singh 16 May '24

16 May '24

Hi Elaine, Is it possible in chimera/chimeraX to display angles between two covalent bonds like in pymol? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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"H-Bonds" Tool Displays Non-H Bond Bonds?
by Melisa Kalaba 15 May '24

15 May '24

Hello. I wanted to display the hydrogen bonds between my ligand and protein, however when I hovered over the displayed bonds with my cursor I noticed one of the bonds being between two nitrogen atoms and I was confused. Is this a bug within the software? I'll attach a screenhot so you can take a look at it yourself: https://drive.google.com/file/d/1N5YRncOrrJnEVRpM8XD7O1tPG02ZTu8G/view?usp=…

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Missing-structure labels
by Eric Pettersen 15 May '24

15 May '24

Hi all, In the 1.9 daily build only (not the 1.8 release candidate), missing-structure pseudobonds are now labeled with the number of residues the pseudobond represents. If you do not like this new behavior, you can turn it off in the 'Labels' preference category (make sure to 'Save' your changed setting). --Eric Eric Pettersen UCSF Computer Graphics Lab

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Alphafold3 models
by Allen Place 15 May '24

15 May '24

I just ran Alphafold3 predictions on our dinoflagellate pks proteins. Will chimerax read the models which are .cif files? I want to highlight the various domains in the 3D models. I am running on OSx. Al Allen R. Place(he/him/his) Professor, Associate Director of Research, Director of BASLab, Director of HAB-CTI Institute of Marine and Environmental Technology University of Maryland Center for Environmental Sciences The Rita Rossi Colwell Center 701 East Pratt Street Baltimore, MD 21202 410-234-8828 place(a)umces.edu ALAN, ALLAN, ALLEN From the Gaelic word for “cheerful” He is smart, makes friends easily, and never loses his sense of humour. He thrives on a challenge Sign up to receive our quarterly newsletter, Inside IMET!

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Cofr command output in log
by Kumpula, Esa-Pekka 15 May '24

15 May '24

Dear ChimeraX crew, A minor quality-of-life improvement request: would it be possible to have the command cofr output the values as a comma-separated list instead of a whitespace separated one? I am including cofr information reatively often in my figure preparation scripts and having NOT to always replace these when copy&pasting would be a nice improvement! Also, in general, can I customize the output of commands to the log (such as view matrix, cofr, zoom, clip list) within an alias for example? In a fluffy dream world, I would have an output from these that I can directly copy&paste to my scripts and get the camera positioned Just Right. Cheers, EP -- Esa-Pekka Kumpula, PhD Senior Postdoctoral Researcher Laboratory of Structural Biology Institute of Biotechnology Helsinki Institute of Life Science HiLIFE University of Helsinki www.helsinki.fi/lsb<http://www.helsinki.fi/lsb>

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Feature request for .glb files
by Leonardo BETANCURT ANZOLA 15 May '24

15 May '24

Hello! I am currently exporting .glb files so I can add them to a Keynote presentation and would like to keep the labels for the amino acids. When I see the file, the letters are in 2d, do you know if there is a way to add a little bit of depth to the letters when exporting such a file? I added a video that shows how the labels are invisible from some points of view Also, it would be awesome if files could be exported in .usdz so they can be easily added to Keynote Thank you, Leo B

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Fwd: Inquiries on UCFS Chimerax
by Tom Goddard 14 May '24

14 May '24

Please send ChimeraX questions to the mailing list unless they contain private data. Begin forwarded message: From: ahmed morsy Subject: Inquiries on UCFS Chimerax Date: May 7, 2024 at 4:52:22 AM PDT To: "goddard(a)cgl.ucsf.edu" Reply-To: ahmed morsy Dear Dr. Thomas Goddard, I hope this message finds you well. I am very thankful for your great tutorial on the UCFS Chimerax YouTube channel. I have a few questions that need your kind response: 1- Can we apply UCFS Chimerax for detecting the interaction between protein & ligand, or small molecule (from Pubchem library) and protein? 2- What is your standard for increasing or decreasing C-alpha distance (in Angestrom) to color the structure that is different between the Alphafold prediction and the experimental one? Thank you for reading my message, and I look forward to hearing from you. Best regards, Ahmed Morsy ========================= Ahmed Morsy, Ph.D. Assistant Professor, Department of Stem Cell & Regenerative Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea Tel.: 02-450-0498 C.P.: +82/10-5299-5844 E-mail: ahmed_morsy86(a)yahoo.com; ahmed(a)konkuk.ac.kr Orcid id: https://orcid.org/0000-0003-3873-9903 Scopus id: 55258308400 (https://www.scopus.com/authid/detail.uri?authorId=55258308400) Researchgate: https://www.researchgate.net/profile/Ahmed-Abdal-Dayem GoogleScholar: https://scholar.google.co.kr/citations?user=NevFBgMAAAAJ&hl=en

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Re: Protein-ligand interactions
by Guillaume Gaullier 14 May '24

14 May '24

Hello Ahmed, I am not aware of any formal standard for figures, at least in my field, beyond the specific technical requirements of different journals (certain preferred image formats with a certain minimal resolution in DPI, etc.). In practice, the reviewers will complain if they find the figures confusing. So the best you can do initially is to use your judgment as to whether the figures show what you want to communicate. It is often very enlightening to run the figures past colleagues who were not involved in the project and see what their first reaction is (do they immediately get what you are trying to show? do they get confused? can they suggest ways to clarify the figures?). Then once you get feedback from reviewers, what needs to be changed typically becomes clear. Regarding aesthetics, pretty much anything goes as long as it doesn’t confuse the message the figure is meant to communicate. In certain fields, there are conventional color codes that have been in use for a long time, and it often facilitates communication with this research community to follow their conventions (even though nobody can force you to do it; a reviewer could suggest it but I believe it would be wrong for them to make it a strict requirement). But this is never advertised anywhere, you need to find out by reading the literature of this specific field. It is always good if figures are reproducible, and I like using ChimeraX’s command scripts for that (see some examples from my own work here: https://github.com/Guillawme/chimerax-viz ). I hope this helps, Guillaume On 11 May 2024, at 16:17, ahmed morsy via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. Dear Dr. Meng, I hope this message finds you well. I am writing to you as we are planning to utilize ChimeraX for structural analysis in our upcoming research projects. As we prepare to integrate ChimeraX into our workflow, we are particularly keen to ensure that our approach and the resulting figures are in line with scientific standards and will be well-received by the academic community. To this end, we would greatly appreciate if you could provide us with any references or examples of published research where ChimeraX has been used for similar purposes. Specifically, we are looking for insights into how figures generated using ChimeraX have been formatted and validated in peer-reviewed publications. We aim to adhere closely to best practices and ensure that our use of ChimeraX enhances the credibility and scientific rigor of our findings. Any guidance, examples, or recommendations you could share would be immensely helpful. Thank you for your time and support. We look forward to your response and any assistance you can provide. Best regards, Ahmed Morsy On Wednesday, May 8, 2024 at 03:31:21 AM GMT+9, Elaine Meng <meng(a)cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: Dear Ahmed Morsy, (1) Depends what you mean by "detecting" ... if you mean will it dock the ligand with the protein to predict where/how it binds, the answer is no. If you mean you already have a structure of a ligand-protein complex (such as from experimentally determined structures or the output of some other protein-ligand docking program), then the answer is yes, you can use ChimeraX to analyze the interactions. For examples of what you could do, see the "protein-ligand binding sites" tutorial: <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html> See also the ViewDockX tool for looking at results output from other programs that do protein-ligand docking: <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html> (2) there is no standard. You have to use your own scientific (and for a paper figure, artistic) judgment, based on what you are trying to show and the details of the proteins you are interested in. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On May 7, 2024, at 10:45 AM, Tom Goddard via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: > > Please send ChimeraX questions to the mailing list unless they contain private data. > > Begin forwarded message: > > From: ahmed morsy > Subject: Inquiries on UCFS Chimerax > Date: May 7, 2024 at 4:52:22 AM PDT > To: "goddard(a)cgl.ucsf.edu<mailto:goddard@cgl.ucsf.edu>" > Reply-To: ahmed morsy > > Dear Dr. Thomas Goddard, > > I hope this message finds you well. > I am very thankful for your great tutorial on the UCFS Chimerax YouTube channel. > > I have a few questions that need your kind response: > > 1- Can we apply UCFS Chimerax for detecting the interaction between protein & ligand, or small molecule (from Pubchem library) and protein? > 2- What is your standard for increasing or decreasing C-alpha distance (in Angestrom) to color the structure that is different between the Alphafold prediction and the experimental one? > > > Thank you for reading my message, and I look forward to hearing from you. > > Best regards, > Ahmed Morsy > ========================= > Ahmed Morsy, Ph.D. > > Assistant Professor, > Department of Stem Cell & Regenerative Biotechnology, > Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea > Tel.: 02-450-0498 > C.P.: +82/10-5299-5844 > E-mail: ahmed_morsy86(a)yahoo.com<mailto:ahmed_morsy86@yahoo.com>; ahmed(a)konkuk.ac.kr<mailto:ahmed@konkuk.ac.kr> > Orcid id: https://orcid.org/0000-0003-3873-9903 > Scopus id: 55258308400 (https://www.scopus.com/authid/detail.uri?authorId=55258308400) > Researchgate: https://www.researchgate.net/profile/Ahmed-Abdal-Dayem > GoogleScholar: https://scholar.google.co.kr/citations?user=NevFBgMAAAAJ&hl=en > _______________________________________________ ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Questions about ChimeraX
by Joshua Hori 13 May '24

13 May '24

Hello ChimeraX, I wanted to reach out and inquire about the ChimeraX tool. I see that it has the ability to save in multiple different formats, but I have a question about conversion into alternative formats. I found details about this tool looking for a PDB to STL file conversion and came across this page: https://www.cgl.ucsf.edu/chimerax/ and looking at the filetypes you interact with listed on this page: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html I see that it works with PDB files, which are used for modeling in some VR and AR environments such as Calcflow and Nanome. Would ChimeraX have the ability to import PDB files and export them as STL files for 3D printing? I ask this as I research ways to make AR and VR more accessible to classrooms. Sincerely, Joshua Hori Accessible Technology Coordinator Information Educational Technology Academic Technology Services 50 Hutchison Dr. Davis, CA 95616 530-752-2439 Schedule a meeting via Calendly<https://calendly.com/d/ytt-hsj-vbn>

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Re: Alphafold 3
by Tom Goddard 13 May '24

13 May '24

Oliver Clarke points out that VP of research at DeepMind, Pushmeet Kohli, says they hope to release AlphaFold 3 code in 6 months. "We love the excitement & results from the community on AlphaFold 3 and are doubling the AF Server daily job limit to 20. Happy to also share that we're working on releasing the AF3 model (incl weights) for academic use, which doesn’t depend on our research infra, within 6 months. Pushmeet Kohli. 11:27 AM · May 13, 2024" https://x.com/pushmeet/status/1790086453520691657 If that happens we will try to add ChimeraX support for running AlphaFold 3 predictions. Tom > On May 13, 2024, at 1:42 PM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > > Hi Tom, hope all is well! It seems like this stance might change (maybe because of all the pushback from the community?): > > https://x.com/pushmeet/status/1790086453520691657 > > So maybe it will be possible by the end of the year... > > Cheers > Oli > >> On May 13, 2024, at 4:23 PM, Tom Goddard via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hi Sohail, >> >> Google did not released the code for AlphaFold 3 so the only way to run it is from their web page. They also have not provide a web service that would allow programs like ChimeraX to submit prediction jobs. I asked a contact at Google DeepMind if they plan in the future to provide a web service or provide the code, and they said they have no plans to do so at this time. Details here >> >> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15135 >> >> Google also is not allowing researchers to run predictions with small molecule ligands except for some very common ones like ATP. It appears Google is treating AlphaFold 3 as a commercial product so the most useful capabilities will only be accessible to the drug discovery company Google has formed called Isomorphic Labs. >> >> I will be making the ChimeraX display of predicted aligned error (PAE) work with AlphaFold 3 output. Currently it is broken because AlphaFold 3 now has predicted aligned error for individual atoms of ligands, ions, glycosylation and non-standard residues while AlphaFold 2 only had values for residues of proteins. I expect to put this fix in ChimeraX today or tomorrow and it will be in the ChimeraX daily builds and ChimeraX 1.8 release candidates. >> >> Tom >> >> >> >> >>> On May 11, 2024, at 6:18 AM, Khawar Siddiqui via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> Hi, >>> Greetings! When ChimeraX will get Alphafold 3? >>> >>> Thanks and best wishes >>> >>> Dr K Sohail Siddiqui, >>> School of Biotechnology and Biomolecular Sciences (BABS), >>> Room 420, Building D26, >>> The University of New South Wales (UNSW), >>> Randwick, High Street, Sydney, Australia. NSW 2052 >>> Office: +61 2 938 55193 <tel:+61 2 938 55193> >>> email: z3030204(a)ad.unsw.edu.au; sohailsiddiqui1995(a)yahoo.com >>> _______________________________________________ >>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >> >> _______________________________________________ >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >

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Alphafold 3
by Khawar Siddiqui 13 May '24

13 May '24

Hi, Greetings! When ChimeraX will get Alphafold 3? Thanks and best wishes Dr K Sohail Siddiqui, School of Biotechnology and Biomolecular Sciences (BABS), Room 420, Building D26, The University of New South Wales (UNSW), Randwick, High Street, Sydney, Australia. NSW 2052 Office: +61 2 938 55193<tel:+61%202%20938%2055193> email: z3030204(a)ad.unsw.edu.au; sohailsiddiqui1995(a)yahoo.com

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Preparing molecular structures for panel of figures
by Prathvi Singh 10 May '24

10 May '24

Hi Elaine, I want to create a panel containing 4 figures. Each figure in the panel will be a ball and sticks representation of an amino acid residue. I have tried using the "Tile Structures" feature in UCSF chimera to create the panel. Although it does ease the job a lot, I find it difficult in aligning residue labels or 2D labels. Is there a grid based feature which can display a grid on the chimera workspace so that I can use its lines as a guide to better align my labels? Thanks in advance Prathvi, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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How can I modify the palette of alphafold?
by Xiaohua Hu 10 May '24

10 May '24

I run command "color bfactor #1 palette alphafold", but I think the color is not so good. How can I modify or redefine the palette alphafold?

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ChimeraX / Alphafold docking question: Heterodimer and ligand
by Anthony Newcombe 08 May '24

08 May '24

Hello I'm currently evaluating ChimeraX for non-commercial use. I'm interested in predicting a complex of an unknown ligand to a heterodimer (receptor) with a known structure, pdb file available. The help files mention: *For predicting a complex (multimer), the sequences of all chains in the complex must be given. The same sequence must be given multiple times if it occurs in multiple copies in the complex. The sequences can be specified either collectively as a model number chosen from the menu of currently open models (e.g. when that model contains multiple chains)* If I download the structure of the heterodimer first, does this mean I can then select this then add the primary sequence of the ligand to try to dock? If not, can I add all the primary sequences and tick 'use PDB templates when predicting structures'? Would this then use the known experimental structure of the receptor? I hope this makes sense and thanks for the help Best wishes Tony Anthony Newcombe Ballinascarthy Clonakilty Cork Ireland

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Fwd: registration issue
by Elaine Meng 08 May '24

08 May '24

Hi Stephen, For questions that don't relate directly to commercial licensing, please use chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (already CC'd here so you don't need to do it) or chimerax-bugs(a)cgl.ucsf.edu <mailto:chimerax-bugs@cgl.ucsf.edu> .... I don't know the answer to your question but the people on those lists would be your best bet. See the "contact us" page: <https://rbvi.ucsf.edu/chimerax/docs/contact.html <https://rbvi.ucsf.edu/chimerax/docs/contact.html>> If I had to guess, I would say that our server was temporarily down and that as soon as it is up (which may actually be the case), your registration attempt will "take" and you won't be prompted again in the near future. As the dialog says, please try again, although I know it's annoying if the server is still down. Maybe somebody on our team can respond as to whether it is up now? In the meanwhile, very sorry for the inconvenience and wasted time filling out the form. Best regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > From: Stephen Miller <miller.stephen(a)gene.com <mailto:miller.stephen@gene.com>> > Sent: Monday, May 6, 2024 3:14 PM > Subject: registration issue > > Hello, I use a ChimeraX license through Genentech, and recently had to swap out my computer due to an issue and had to reinstall the program. I've been getting a notification to register but when I submit the information it says the registration > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > ZjQcmQRYFpfptBannerEnd > Hello, > > I use a ChimeraX license through Genentech, and recently had to swap out my computer due to an issue and had to reinstall the program. I've been getting a notification to register but when I submit the information it says the registration server is unavailable, and then the notification pops up the next time I launch the program. > > Is there something I can do to get this done properly? Thank you for any help! > -Steve > >

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Re: [Chimera-users] Chimera scripting
by Elaine Meng 07 May '24

07 May '24

Hi Flip, If you save a PDB file from ChimeraX it will save the current helix and strand assignments of the protein and peptide residues (as HELIX and SHEET records). I'm not sure if that is what you were saying is missing, or how you determined that they were missing. It does not save, however, helix type or which sheets the strands belong to. Elaine > On May 7, 2024, at 11:29 AM, Flip Jansen <f.bastiaanjansen(a)gmail.com> wrote: > > Hi Elaine, > > Thank you that is very clear! > > As for the second point, I meant preserving secondary structure information when saving an adapted PDB file in Chimera. I am now planning on using PyMOL for this purpose. > > Thanks again for your help! > > Best, > Flip > > On Mon, May 6, 2024 at 11:56 AM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hello Flip, > (1) we would generally recommend using ChimeraX over Chimera for many reasons: performance, enhanced features, current development and support. The rest of this answer applies to ChimeraX so I'm putting it on the chimerax-users list. > > (2) you can create a blank cubic grid first with "volume new" and then refer to that in the "molmap" command "onGrid" option. > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#new> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html> > > (3) I do not understand what you mean by losing secondary structure information when saving a map. Only atomic structures (not maps) have secondary structure information, i.e. helix and strand assignments. Can you clarify? > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On May 6, 2024, at 10:40 AM, Flip Jansen via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > > > Hello Chimera dev team, > > > > I am a junior specialist from across the hall working at the Fraser Lab and I have some questions about using chimera scripting for omitting densities and generating reference maps. > > > > One of the issues I have been having has been that using the molMap function in Chimera generates a non-cubic output and I am aware that I can use onGrid with a pre-existing map with the desired dimensions. However, in the workflow, I am setting up I do not yet have a reference map and I am in most scenarios starting with just a PDB or an adapted from PDB map. > > > > Is there a way to let Chimera(X) generate a cubic output map from PDB without requiring another map from an external program like cryoSPARC? > > > > Another question I have is regarding the loss of secondary structural information when saving a map in Chimera. Is there a way to save a map while maintaining that information? > > > > Any help is highly appreciated, I would also be happy to come by an talk in person. > > > > Best, > > Flip Jansen >

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Guidance on aligning models with overlapping aa subsequences
by Martin Gordon 07 May '24

07 May '24

Hi everyone, I'm hoping to get some assistance from the community for visualizing structures from multiple AF runs with overlapping subsequences. We have been using AlphaFold monomer to try to identify structure and domains of a large (+3000aa) human protein. Our AF runs fail to model the full structure (possibly insufficient resources), so we have tried 'breaking' up the protein into overlapping subsequences. I was wondering if there is a sensible way to combine these substructures based on their overlapping regions? I have tried matchmaker, which I believe constructs a MSA and attempts to align the structures, but it seems a significant region of the overlap is not aligning correctly (img below with the overlapping subsequences highlighted). Any guidance is greatly appreciated. Thank you, Martin [image: image.png] Thank you, Martin

3 3

Inquiry on the vertex_convexity function
by Yoseph Loyd 07 May '24

07 May '24

Hi ChimeraX Team, My name is Yoseph, I'm a student. I saw that your measure convexity function 'vertex_convexity' is documented to report the vertex convexity from ' 2pi - half cone angle of the incident vertex and all triangles the incident vertex is a part of'. Is the half cone angle generated by averaging all half cone angles? Thank you for taking the time to read this and I hope your day goes well. Best regards, Yoseph Loyd

2 2

Making movie of whole cell model with EM images
by George Schaible 07 May '24

07 May '24

Hello, My name is George Schaible and I am a post doc at Montana State University. I would like to use ChimeraX to make my movies of whole cell serial block face EM data I have modeled in IMOD/3dmod and I was wondering if someone could point me towards a tutorial or some way that I can make the movie using both the model and the original EM data. Any information is helpful and thank you! -- George A. Schaible, Ph.D Dept. of Chemistry & Biochemistry Montana State University Google Scholar profile <https://scholar.google.com/citations?user=_M2xvYIAAAAJ&hl=en>

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No version number in Add- Remove Program (Windows)
by Gruhm, Sebastian 07 May '24

07 May '24

Hello, I manage the software distribution at the Frei Universität Berlin, and I noticed that after installing ChimeraX 1.7.1, the entry in "Add-Remove Programs" (ARP) does not include a version number (see attached Screenshot). This is problematic because I cannot create a query for the version number in the software distribution (SCCM). All that would need to be done to display the version number under ARP is to create the RegKey "DisplayVersion" under "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall\UCSF ChimeraX_is1". Would be great to see this implemented in the next version of ChimeraX. Mit freundlichem Gruß Sebastian Gruhm [cid:image001.jpg@01DAA061.0DA8A940] Zentraleinrichtung für Datenverarbeitung Server Infrastructure (SI) Fabeckstraße 32, 14195 Berlin Raum: 110 Phone: +49 30 838 58668 sebastian.gruhm(a)fu-berlin.de

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Adjust the Rotation Axis Size in ChimeraX
by AARON FERRELL 07 May '24

07 May '24

Hello, Is there a way to adjust the size of the rotation axis generated by the command line "measure rotation #2 toModel #1, in ChimeraX? I am looking to adjust both the length and diameter of the axis display. Please let me know! Best, Aaron

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Issue with Recurring Update Notifications in ChimeraX
by ahmed morsy 07 May '24

07 May '24

Dear ChimeraX Support Team, I hope this message finds you well. I am writing to ask for help with an ongoing issue I've been having with ChimeraX. Despite having downloaded and installed the most recent version of ChimeraX, I continually receive prompts to update the software each time I launch it. This occurs even though I am certain I am running the latest version. Could you please help me understand why this might be happening, and advise on how to resolve this issue? It would be helpful if you could provide steps or recommendations to ensure that the software recognizes the current version installed on my system. Thank you for your time and assistance. I look forward to your prompt response. Best regards,Ahmed Morsy=========================Ahmed Morsy, Ph.D. Assistant Professor, Department of Stem Cell & Regenerative Biotechnology,Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, KoreaTel.: 02-450-0498C.P.: +82/10-5299-5844E-mail: ahmed_morsy86(a)yahoo.com; ahmed(a)konkuk.ac.kr Orcid id: https://orcid.org/0000-0003-3873-9903 Scopus id: 55258308400 (https://www.scopus.com/authid/detail.uri?authorId=55258308400) Researchgate: https://www.researchgate.net/profile/Ahmed-Abdal-Dayem GoogleScholar: https://scholar.google.co.kr/citations?user=NevFBgMAAAAJ&hl=en

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Alphafold
by Chang, Jufang 07 May '24

07 May '24

Dear Sir Recently I can not use the ChimerX to do the alphafold prediction. The error message is some connection to the colab is broken sine March 2024. I am wondering when this feature of ChimeraX will come back? Thank you Ju-Fang ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Amber output pdb file - can't open... bad PDB record
by Alexander Hung Lee 06 May '24

06 May '24

Hi! I have a large system containing >100k atoms w/o water. Amber produced a pdb file, and I have a trajectory file for it. When I try to open the pdb in chimeraX, most of it loads but with warning "Ignoted bad PDB record on line xxx" and it's all for atom # > 9,999. As a result, when I try to open the .nc file along with the pdb file, the # of atoms don't match anymore. 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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Re: [Chimera-users] Chimera scripting
by Elaine Meng 06 May '24

06 May '24

Hello Flip, (1) we would generally recommend using ChimeraX over Chimera for many reasons: performance, enhanced features, current development and support. The rest of this answer applies to ChimeraX so I'm putting it on the chimerax-users list. (2) you can create a blank cubic grid first with "volume new" and then refer to that in the "molmap" command "onGrid" option. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#new> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html> (3) I do not understand what you mean by losing secondary structure information when saving a map. Only atomic structures (not maps) have secondary structure information, i.e. helix and strand assignments. Can you clarify? I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 6, 2024, at 10:40 AM, Flip Jansen via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello Chimera dev team, > > I am a junior specialist from across the hall working at the Fraser Lab and I have some questions about using chimera scripting for omitting densities and generating reference maps. > > One of the issues I have been having has been that using the molMap function in Chimera generates a non-cubic output and I am aware that I can use onGrid with a pre-existing map with the desired dimensions. However, in the workflow, I am setting up I do not yet have a reference map and I am in most scenarios starting with just a PDB or an adapted from PDB map. > > Is there a way to let Chimera(X) generate a cubic output map from PDB without requiring another map from an external program like cryoSPARC? > > Another question I have is regarding the loss of secondary structural information when saving a map in Chimera. Is there a way to save a map while maintaining that information? > > Any help is highly appreciated, I would also be happy to come by an talk in person. > > Best, > Flip Jansen

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session files question
by Krishnan Raman 06 May '24

06 May '24

I have two large session files (1-2 GB). Is there any way to combine them ? thanks Krish CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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Error when opening multiple tiff stacks (32-bit)
by Christophe Leterrier 03 May '24

03 May '24

Hi, I have two 32-bit tiff stacks (generated by ImageJ) and I try to open both to overlay two channels. When opening the second one or trying to open both at the same time (see paths below), I get the following error with the latest stable and daily ChimeraX macOS versions: UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX open "/Users/christo/Travail/Data NSTORM/230811 Patt#56/Figure 4 Article (actin DNA-Paint bass)/3um aligned 3D/Recs TS ROIs 3um aligned (Gxy4z4)/Roi002_C2_N04_ch1_ph647_bas643_sypto_map_3D_48K_DC1C_(22688,12672)_TS3D.tif" "/Users/christo/Travail/Data NSTORM/230811 Patt#56/Figure 4 Article (actin DNA-Paint bass)/3um aligned 3D/Recs TS ROIs 3um aligned (Gxy4z4)/Roi002_C2_N04_ch2_ph647_bas643_sypto_map_3D_7,63K_DC1C_transfo_(22688,12672)_TS3D.tif"Traceback (most recent call last): File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py", line 334, in _qt_safe run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + ("" File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 191, in provider_open models, status = collated_open(session, None, paths, data_format, _add_models, log_errors, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 513, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/__init__.py", line 182, in open return open_map(session, path, format=_name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 3621, in open_map smodels, smsg = open_grids(session, sgrids, name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 3723, in open_grids v.update_drawings() File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 813, in update_drawings self.image_levels, self.image_colors = self.initial_image_levels() ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 633, in initial_image_levels mstats = self.matrix_value_statistics() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 1734, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 1769, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 1252, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 1276, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map_data/griddata.py", line 317, in matrix m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map_data/imagestack/imagej_tiff.py", line 74, in read_matrix a = pi.planes_data(klist, cc, ch, self.time) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map_data/imagestack/imagej_tiff.py", line 199, in planes_data a = tif.asarray(key = plist) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py", line 4272, in asarray pages = pages._getlist(key) ^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py", line 7532, in _getlist pages = [getitem(i, validate=validhash) for i in key] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py", line 7532, in <listcomp> pages = [getitem(i, validate=validhash) for i in key] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py", line 7578, in _getitem self._seek(key) File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py", line 7481, in _seek raise IndexError('index out of range') IndexError: index out of range IndexError: index out of range File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py", line 7481, in _seek raise IndexError('index out of range') See log for complete Python traceback. Any idea of what is going wrong?

2 3

[Query] Possible to control tool panel size programmatically?
by leeyang+chimerax＠gmail.com 03 May '24

03 May '24

Hi, Not a feature request but a query. Is there currently a way to change tool panel sizes with a command, either in absolute terms or as a fraction of another parameter value? Cheers, Yang

3 4

Installing ChimeraX on Ubuntu 24.04 LTS
by mborgnia＠gmail.com 02 May '24

02 May '24

Hi all, I got a shiny new machine with Ubuntu 24.04 LTS, unfortunately the regular repositories do not include libffi7 and that causes a failure when installing the 22.04 package. I have also tried to run the generic Linux 64 bit version but fails to load because the libffi.so.6 file is not found. Any ideas on how to proceed? Thanks Mario J. Borgnia

3 6

Using chimerax library code outside of the GUI
by Artie Kushner 02 May '24

02 May '24

Hi, I apologize sincerely since I imagine this comes up often on the mailing list. I'm basically wondering if it's possible to import just the `core` functionality from a chimerax installation into a custom python environment and bypass the GUI and the binary completely. Example: I don't think it matters whether it's linux, mac, or source build, but let's say i installed a clean chimerax via my package manager (`yay i chimerax`). It's at `/opt/chimerax` and looks like this: (venv) ᢹ ritual.rtviii[ /opt/chimerax ] ls -la total 24 drwxr-xr-x 6 root root 4096 May 1 16:08 . drwxr-xr-x 10 root root 4096 May 1 16:58 .. drwxr-xr-x 4 root root 4096 May 1 16:51 bin drwxr-xr-x 8 root root 4096 May 1 16:51 include drwxr-xr-x 4 root root 4096 May 1 16:51 lib drwxr-xr-x 6 root root 4096 May 1 16:51 share If I launch `chimerax` at the command line, i get a functional GUI etc. It works. I create a fresh custom `virtualenv` with the same python that this chimerax ships: virtualenv --python='/opt/chimerax/bin/python3.11' venv Then i do something ugly in the name of science: i symlink the chimerax folder from the installation into my virtualenv: ln -s /opt/chimerax/lib/python3.11/site-packages/chimerax /home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-packages/chimerax i also tried: for P in $(ls /opt/chimerax/lib/python3.11/site-packages/); do ln -s /opt/chimerax/lib/python3.11/site-packages/$P /home/rtviii/dev/try_chimerax/ venv/lib/python3.11/site-packages/$P; done This enables me to import chimerax modules into my python code that uses this virtualenv: ```/home/rtviii/dev/try_chimerax/test.py from chimerax.core.commands import run from chimerax.core.session import Session import chimerax.mmcif.mmcif as mmcif s = Session("Hi") print(s) run(s,"open 1ubq.cif") ``` However, this is where i'm struggling a little to use any actual functionality (especially interested in cutting, merging structures and operations treating density maps and mmcif structures) because the Session wouldn't initialize well: ``` <chimerax.core.session.Session object at 0x70472673b5d0> NOTE: Traceback (most recent call last): File "/home/rtviii/dev/try_chimerax/test.py", line 9, in <module> run(s,"open 1ubq.cif") File "/home/rtviii/dev/try_chimerax/venv/lib/python3.11/site- packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2849, in run _compute_available_commands(session) File "/home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2431, in _compute_available_commands ts.register_available_commands(session.logger) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute'register_available_commands' BUG: AttributeError: 'NoneType' object has no attribute'register_available_commands' File "/home/rtviii/dev/try_chimerax/venv/lib/python3.11/site- packages/chimerax/core/commands/cli.py", line 2431, in _compute_available_commands ts.register_available_commands(session.logger) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ _See log for complete Python traceback._ ``` I had some success with a similar approach in PyMol in this regard, but can't quite get this to work in ChimeraX. I really appreciate any advice for achieving this scripting decoupling from GUI/binary if that's possible at all: - either how to "pull in" ChimeraX library code properly (i realize mine is an ugly hack) - how to use library code otherwise - how to bypass the dependence of a lot of commands on the Session object or how to initialize it outside of the gui properly: an example of how to use selections to open a local density map and perform a smoothing, for example. Kindest regards and huge thanks for the monumental application. Artem, UBC Vancouver

2 1

Problem visualizing hydrogen bonds during a trajectory
by Ute Roehrig 02 May '24

02 May '24

Hello, I'm trying to visualize the hydrogen bonds of a small molecule in water over the trajectory of a molecular dynamics simulation, using the following commands: alias evalhb hide solvent; hb :LIG reveal true coordsets false makePseudobonds true ; view perframe evalhb; coordset #1 1,20 holdsteady :LIG; wait 20; ~perframe However, this does not work as expected. Could you please help me with this issue? Thank you, Ute

2 2

Visualizing PAE contact lines between more than two peptides
by David S. Fay 30 Apr '24

30 Apr '24

Greetings, Was wondering if it’s possible to simultaneously display PAE contact lines for more than two peptides? For example, all contacts between A and B AND B and C etc. Couldn’t find anything on it and have already made the obvious attempts such as "alphafold contacts /A to /C AND /B to /C distance 6” Thanks! David

2 2

Schematic
by Das, Abhinaba 30 Apr '24

30 Apr '24

Hi all, I don’t think it is possible to draw this kind of schematic representation (panel b) in ChimeraX, is it? [cid:image001.png@01DA9A41.C6E2E040] Thanks, Abhi

3 2

Alphafold predicton using ChimeraX
by Chang, Jufang 29 Apr '24

29 Apr '24

Dear Sir, When I tried to use alphafold prediction with ChimeraX, I got this error message. I alreday download the latest version 1.7.1 (2024-01-23). But I still got the same error message. Could you please suggest me what to do the next to fix this? Thank you Ju-Fang AlphaFold Prediction Requires Newer ChimeraX Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or later. The ChimeraX AlphaFold prediction service was broken by an update on Google Colab on March 14, 2024. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

2 1

running AlphaFold predictions in ChimeraX
by Elaine Meng 29 Apr '24

29 Apr '24

> On Apr 29, 2024, at 9:31 AM, Chang, Jufang via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Greg > > Recently I can not use the ChimerX to do the alphafold prediction. The error message is some connection to the colab is broken sine March 2024. I am wondering when this feature of ChimeraX will come back? > > Thank you > > Ju-Fang Hello Ju-Fang, As Greg said, you should use the address chimerax-users(a)cgl.ucsf.edu for ChimeraX questions, not chimera-users(a)cgl.ucsf.edu which is for Chimera, and put some description of the current issue in the email subject line. If you get an error running the AlphaFold prediction in ChimeraX and you think it is a bug, please use ChimeraX menu Help... Report a Bug and include a description and your email address. As far as I knew it was working, so we wouldn't know what the problem is for you without more information. Also here are some common issues and limitations of running these predictions: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#caveats> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

2 3

Unroll radius?
by Ricardo Righetto 29 Apr '24

29 Apr '24

Hi, We've been using the 'volume unroll' command on a cylindrical structure, and while we do get some very decent results with the defaults, we want to do a systematic comparison with values entered manually for the inner and outer radius. Specifically, I'd like to know if I can get ChimeraX to report what minimum and maximum radii it is currently using for unrolling the volume? Currently, all I get in the reply log is this: volume unroll #1 Opened unrolled SPA_density.mrc as #2, grid size 68,697,492, pixel 1.22,1.2,1.2, shown at step 1, values float32 https://www.cgl.ucsf.edu/chimera/data/downloads/1.8/docs/UsersGuide/midas/v… From the help here it says: > (...) and inner and outer radii *r1* and *r2* (defaults are 90% of the > smallest radius and 110% of the largest radius of the displayed isosurface, > respectively, given the cylinder center and axis direction). Since this is a high-resolution cryo-EM map with many intricate features, it's hard to visually find exactly what are the smallest and largest radii currently displayed at the isosurface. So we'd like to know what ChimeraX is finding by itself and compare it to our measurements. Any tips are appreciated. Thank you! -- Ricardo Diogo Righetto

2 4

Glb files
by Rowe-Magnus, Dean 28 Apr '24

28 Apr '24

Hello, Can you please tell me how to save a .glb file as a .pdb so that I can use Matchmaker to align the structures? Thank you, Dean

2 1

How to show van der Waals surface
by 我就要柠乐 26 Apr '24

26 Apr '24

Dear Sir/Madam         Recently, I have been using ChimeraX for graphical analysis, and I find the software to be very user-friendly and efficient. I am currently facing a challenge where I want to display the van der Waals surface of a residue, similar to this illustration（https://doi.org/10.1038/s41467-022-31526-7）. However, I am not quite sure how to write the command correctly. I have looked up the commands on the official website and tried using these two:surface #1:230； surface style mesh. The bottom is open （the rad circle）, but I would like to have a complete van der Waals surface with closed openings, similar to what is typically seen in the literature. I would appreciate your assistance. Thank you！                                                                                                                       yours  sincerely                                                                                                                       yiwen 我就要柠乐 790639436(a)qq.com  

2 2

Question about visualisation of DNA structure
by Enrico Martinez 26 Apr '24

26 Apr '24

Dear Chimera-X users, I have a question about the visualisation of the DNA structure obtained after tleap processing for Amber. As I have noticed, due to the renaming of the DNA residues, some of the sugar parts are not correctly recognised by Chimera-X (see the attached screenshot) and so these elements are only displayed as organic ligands. Would it be possible to change its style using some commands, assuming that the names of the residues located at the terminal parts of the DNA helix are DC5, DG3 and DT5, DT3 (so that Amber adds numbers to them)? Would it be possible to change the style of all the residues e.g. showing them ass ring fills or like a color bricks (default vizualisation which looks very cool!) using selection expressions like :DT*,DG*,DC*,DA* ? Many thanks in advance ! Enrico

2 7

Add options to snapshot command
by Jaremko, Matt Joseph 26 Apr '24

26 Apr '24

Hello ChimeraX Team, Can you add option to snapshot command like transparentBackground and height to allow more customization of this convenient tool? Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 126 E Lincoln Ave | 80B 1012 | Rahway, NJ 07065 Cell: 808.741.6277 | Email: matt.jaremko(a)merck.com<mailto:matt.jaremko@merck.com> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

3 3

palette command
by Cairns, Claudia Anna 26 Apr '24

26 Apr '24

Dear sir or madam, I try to apply the palette command to change the color range of the mlp command. Unfortunatelly i always get an error. For "palette rainbow" for example I get: rainbow Unknown command: palette rainbow Can you please help me? Sincerely, Claudia Cairns M.Sc. (Biotechnology) Department 'Applied and Molecular Microbiology' Institute of Biotechnology - TIB 4/4-1 Technische Universität Berlin Gustav-Meyer-Allee 25 D-13355 Berlin Phone: +49-(0)30-314-72827 E-mail: c.feurstein(a)tu-berlin.de<mailto:carsten.pohl@tu-berlin.de> Web: <http://www.mikrobiologie.tu-berlin.de> https://www.tu.berlin/mikrobiologie/

2 1

Reconstruction of missed loop fragments
by Enrico Martinez 26 Apr '24

26 Apr '24

Dear Chimera-X user! I am preparing a model of GPCR protein for the molecular dynamics simulation. In this structure there is a loop fragment of 10-20 residues which is missed. Is it possible to reconstruct it (e.g. based on the sequence information or alternatively just add manually the missing fragment) using some tool of Chimera-X e.g. combining with the bond command ? Many thanks in advance ! Enrico

2 7

Greek characters
by Marta Martinez 26 Apr '24

26 Apr '24

Hi guys, I just downloaded a pdb file from AlphaFold DB (AF-P69905-F1-model_v4.pdb). After modifying it with ChimeraX (version 1.6.1 (2023-05-09)) I've saved the modified atomic structure as a cif file. The original pdb file contains this line: COMPND 2 MOLECULE: HEMOGLOBIN SUBUNIT ALPHA; After saving the file as cif format ALPHA is not longer a string but a GREEK character: _entity.pdbx_description "hemoglobin subunit α" Is there any flag in the save command that disables this conversion from plain ASCII to UTF-8? Thank you very much for the answer in advance: MARTA -- Marta Martinez Gonzalez Biocomputing Unit (Lab B13) National Center for Biotechnology-CSIC Darwin, 3. Campus de la Universidad Autonoma de Madrid 28049 Madrid. Spain Tel:+34 915854510 Fax:+34 913720112 E-mail: mmmtnez(a)cnb.csic.es

2 1

atom serial_number is inconsistent with PDB serial numbers in multi-chain structure
by Daniel David Richman 26 Apr '24

26 Apr '24

Hi all, I’ve been debugging an off-by one error in a ChimeraX script I’m working on, which I’ve traced to a apparent inconsistency between the serial_number reported by ChimeraX for an atom and the actual serial number of that atom read/written in PDB format. To reproduce: open 5MJ7 select #1/B:6@CA info atoms sel attribute serial_number ==> atom id /B:6@CA serial_number 2548 but the correct serial number for this atom in 5MJ7.pdb is 2549. Maybe this is because the TER record for chain A takes up one serial number in the PDB file, but ChimeraX doesn’t include it as a numbered atom? Regardless, how can I query ChimeraX for the actual serial number that will be written if I write out a PDB file? Thanks, Daniel

3 7

How to make an MD template for ISOLDE?
by Guillaume Gaullier 25 Apr '24

25 Apr '24

Hi Tristan and chimerax-users, Some time ago I asked the list about modeling PTM and got several helpful answer, including this one: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu… Now, I am working on a structure containing chlorophyll A molecules (residue code CLA) and realized that it won’t work for MDFF in ISOLDE because there is no MD template for it. After trying to manually fit one of these molecules rigidly, I concluded that I would rather spend the rest of the month learning how to make an MD template for it (than next month painstakingly fitting every single molecule manually rigidly). From the message linked above, I think this should be doable because this time it is not a covalent modification on an otherwise parameterized residue, but simply a new ligand (ok, maybe the coordinated Mg2+ makes it a bit more complicated?). I looked up ANTECHAMBER, and also some documentation from OpenMM, but that got me nowhere, mostly because I have little clue what the task really entails. My guess is that I need some program to take the CLA residue in PDB or mmCIF format (which I can easily save from a previous PDB entry) and write out an OpenMM XML file like the one you sent me back then for KCX. Is this correct? The ANTECHAMBER documentation mentions many programs and formats, and I got totally confused. If you have time to elaborate a bit on the specific practical steps to take (including how to supply the final XML file to ISOLDE), that would be super helpful! I can do with pointers to documentation, not afraid to read, but I need help getting oriented. Thank you in advance! Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

2 3

Realsense issues
by Casey Eubanks 24 Apr '24

24 Apr '24

Hey guys, You all helped me a week or so ago getting the Realsense package updated to the new version of chimerax, which I can now download so thats great! But I am now having an issue with running its command "Realsense on" I receive the following errors attached to this email It is having errors processing the trigger and it says it cant resolve the requests. Let me know if I am doing anything wrong or need to make any changes! Thanks, Casey Eubanks Service Desk Specialist MOBILE (205) 617-0581 time zone United States, Central Time Zone (CST) [cid:image001.png@01DA9660.03D4DE80]<https://www.biocryst.com/> "Go Fast, Patients are waiting" If you need immediate IT support please submit a ticket to ITsupport(a)biocryst.com<mailto:ITsupport@biocryst.com> CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

2 2

Finding unmodeled blobs in a map
by Guillaume Gaullier 24 Apr '24

24 Apr '24

Hello, With `volume zone` I can show the parts of a map close to an atomic model. Is there a way to do the opposite, i.e. show only the parts of a map that don’t enclose any atoms? This would be already very helpful only as a visualization. But even better would be a way to build a list of markers at the centroids of such unmodeled blobs, to easily navigate to them. Or maybe this is too narrow in scope and better left to ISOLDE? (Sorry Tristan… more feature suggestions…). Thank you, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

3 2

Adding missing atoms of the DNA structure
by Enrico Martinez 24 Apr '24

24 Apr '24

Dear Chimera-X users I am preparing the structure of the protein-DNA complex for molecular dynamics simulation with Amber. This is the original pdb: https://www.rcsb.org/structure/5FKW When I try to parametrize it the tleap shows the following error because of the absence of some atoms from the phosphate: FATAL: Atom .R<DG5 733>.A<P 32> does not have a type. FATAL: Atom .R<DG5 733>.A<OP1 33> does not have a type. FATAL: Atom .R<DG5 733>.A<OP2 34> does not have a type. FATAL: Atom .R<DG5 758>.A<P 32> does not have a type. FATAL: Atom .R<DG5 758>.A<OP1 33> does not have a type. FATAL: Atom .R<DG5 758>.A<OP2 34> does not have a type. Would it be possible to use some commands of the Chimera-X to automatically repair this part of the DNA by adding missing atoms ? Thank you in advance ! Enrico

4 9

Cutting out an asymmetric unit from the map
by Das, Abhinaba 23 Apr '24

23 Apr '24

Hi! I was wondering if there is a sequence of commands one could use to extract an asymmetric unit from the original map after roughly fitting the model into it. The positions of these extracted maps should of course be preserved and should on the same grid. One can then better fit the model in this extracted ASU density. Thanks in advance for any guidance. Abhi

3 2

Lighting options in ChimeraX
by Elaine Meng 23 Apr '24

23 Apr '24

> On Apr 20, 2024, at 7:36 PM, Friedman, Simon <friedmans(a)umkc.edu> wrote: > > I am working on mol graphics for a figure. I'm using both chimera-x and chimera. I'm trying to figure out if chimera-x has a set of functionality that chimera has. Specifically in chimera I was able to move light sources around, change intensity, shinyness etc. Also I was able to use ray tracing in the output. In chimera-x I can't find any menu for moving light sources around etc. One very cool thing that is there is the 'soft' lighting option which gives a very cool surface to the carbon atoms. So I was wondering if there were more options for messing with lighting etc in chimera-x? > Thank you! > > Cheers, > Simon > > Simon H. Friedman, Ph.D. > UM Curators' Distinguished Professor > Division of Pharmacology & Pharmaceutical Sciences > University of Missouri, Kansas City Hey Simon! ChimeraX does not have ray-tracing, but as you discovered with the ChimeraX "soft" lighting (sugar cube icon in the toolbar), it does have ambient-occlusion lighting simulated by multiple multidirectional light sources, which Chimera does not have. The rest of this description pertains to ChimeraX: When you try the different lighting icons in the toolbar, the corresponding command is shown in the Log. So that should help you learn some of the common options. However, there are lots more options available with the commands than are represented by toolbar icons. (1) the "lighting" command has the presets including soft, but also options for intensities, colors and directions of the directional lights (key light and fill light), depth cueing, and shadows, among many other things. There is no GUI for changing the direction interactively, however. See the "lighting" manpage and many options explained therein. It also shows pictures of the relevant icons from the toolbar. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/lighting.html> (2) the "graphics" command has options for background color, silhouette edges (the outlines that are usually black), and triangulation fineness of atom/bond/ribbon representations, see: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html> (3) the "material" command has control over shininess of objects <https://rbvi.ucsf.edu/chimerax/docs/user/commands/material.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

1 0

Running AlphaFold through Chimerax vs. Colab directly
by Coyle, Maxwell C 22 Apr '24

22 Apr '24

Hello! I’ve been predicting structures recently using the AlphaFold tool through ChimeraX (which directs to the alphafold21_predict_colab.ipynb notebook), but I’ve noticed I get often quite different results when I run the same prediction through the AlphaFold.ipynb notebook directly in Colab. I was wondering if anybody could point me to the major differences between these two implementations? Are they searching different libraries to generate a multiple sequence alignment? Are they using different numbers of iterations or energy minimization strategies? Thanks for any guidance, Max Max Coyle, PhD Postdoctoral Fellow, Bellono Lab Dept of Molecular and Cellular Biology Harvard University mcoyle(a)fas.harvard.edu

2 1

transform coordinates of an atomic model
by Engeholm, Maik 22 Apr '24

22 Apr '24

Hi Tom, hi Eric, thanks a lot for answering my previous question so comprehensively! Hope it's OK to bother you again. This is about something completely unrelated. I would like to apply a transformation (rotation plus translation) to an atomic model. I need to change the coordinates of the model relative to the overall coordinate system. Changing the scene or camera coordinates is not an option, since in the end I want to place multiple copies of my model (in this case a nucleosome) in a specific orientation relative to each other (i.e. within the same coordinate system) to model an array of nucleosomes. If I remember correctly, back in Chimera this could be achieved with "model.openState.global/localXform(transformation)" where transformation was an chimera.Xform object. But as far as I can see this is not supported in chimeraX. Here is a reproducible example of the simplest case, in which I define the center and two (roughly) orthogonal axes of my atomic model (i.e. the normal of the DNA superhelix and the dyad axis) and try to map those onto the origin of the coordinate system and two unit vectors. """ from chimerax.core.commands import run import numpy as np from numpy import cross, dot np.set_printoptions(suppress = True) run (session, 'close session') run (session, 'windowsize 360 360') target_centre = np.array((0, 0, 0)) target_normal = np.array((0, 1, 0)) target_dyad = np.array((0, 0, 1)) target_3rd_axis = cross(target_normal, target_dyad) run (session, 'open 3lz0 name 3lz0') pdb3lz0_DNA_plane = run (session, 'define plane #1/I,J:-56-56') pdb3lz0_DNA_centre = run (session, 'define centroid #1/I,J:-56-56') pdb3lz0_dyad_base_pair = run (session, 'define centroid #1/I,J:0') pdb3lz0_dyad_axis = run (session, 'define axis #1.4 #1.5') pdb3lz0_centre = session.models[3].xform_center pdb3lz0_normal = session.models[3].xform_normal pdb3lz0_dyad = session.models[6].xform_direction pdb3lz0_3rd_axis = cross(pdb3lz0_normal, pdb3lz0_dyad) rotation_inverse = np.c_[pdb3lz0_3rd_axis, pdb3lz0_normal, pdb3lz0_dyad] rotation = np.linalg.inv(rotation_inverse) translation = -pdb3lz0_centre transformation = np.c_[rotation, translation] print(session.models[0].position.matrix) """ At this point I have tried to modify the position.matrix with "session.models[0].position.matrix = transformation" but this gives me an "AttributeError: property 'matrix' of 'Place' object has no setter". I'm sure there must be a way to transform an atomic model in this way and would be really grateful for your help. Thanks a lot in advance, Maik

2 1

Re: ChimeraX license and download
by Elaine Meng 20 Apr '24

20 Apr '24

Hi Asma, It is recommended to send ChimeraX questions to chimerax-users(a)cgl.ucsf.edu CC'd here, if the questions do not include any information that needs to be private (i.e. do not include your license key or proprietary data). I don't know all technical aspects of the program. I'm not sure exactly what this error is but the first thing to try is to get a newer version of ChimeraX. As the message says, you are running an extremely old version and probably if you download and use the current version 1.7 this error message will not appear. However, if it does, then you can ask again, or use the usual bug reporting mechanism (ChimeraX menu Help... Report a Bug). I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 16, 2024, at 8:19 AM, Asma Rehman <ARehman(a)Novavax.com> wrote: > > Hi Elaine, > > Good morning, > Hope you’re doing well! > > I was reaching out to ask about the following error that I’m seeing on ChimeraX software- Please suggest! > > Many thanks, > Asma >

2 2

Fwd: ChimeraX Chain Transparency
by Elaine Meng 19 Apr '24

19 Apr '24

Hi Matt, The address for ChimeraX questions is chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here, as mentioned in the "contact us" page: <https://www.rbvi.ucsf.edu/chimerax/docs/contact.html <https://www.rbvi.ucsf.edu/chimerax/docs/contact.html>> Yes, of course you can make some of the atoms transparent and others not. I say "atoms" because at least in your image, you are displaying the atoms in the sphere style. You just need to specify that set of atoms in the transparency command, for example, for atoms of B chain only to be 70% transparent: transparency /B 70 target a ...or you could use menu: Select... Chains... [choose the one that you want] ...and then use command: transparency sel 70 target a The "target a" part means atoms. The default is to change transparency of only molecular surface (target s), so if you omit "target a" nothing happens to the atoms. Of course you can use a different % value than 70. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > > From: Matthew Bubak <Matthew-Bubak(a)omrf.org> > Subject: ChimeraX Chain Transparency > Date: April 18, 2024 at 12:48:22 PM PDT > > Hello, > > I am trying to make specific chains of mitochondrial complexes more or less transparent. I am able to make the entier complex transparent, but not individual chains. For example in the figure below (mitochondrial complex I), I would like to make the purple chains approximately 50% transparent, and the blue chain 90% transperent, and leave the rest untouched. Is this possible? > > > > Thank you for your help, > > Matt Bubak, PhD. > Post-Doctoral Fellow > Aging and Metabolism Program > The Oklahoma Medical Research Foundation

2 1

import from local file in chimerax-python script
by Engeholm, Maik 18 Apr '24

18 Apr '24

Hi there, I'm running a python script either from within ChimeraX (with "open http://myScript.py") or from the command line (using "chimerax http://myScript.py"). As the script gets longer and longer, I would like to store some class definitions in a separate file (http://classDefinitions.py within the same directory as http://myScript.py and then import those into the main script with some command like "from classDefinitions import testClass". This, however, gives me an "ModuleNotFoundError: No module named 'testClass'". What is the correct way to do this? Any help would be much appreciated! Cheers, Maik

3 4

Volume flip issue
by Luca Pellegrini 18 Apr '24

18 Apr '24

Hi, if I flip a map with ‘volume flip #ID', save the flipped map and then open it, the saved copy is noticeably shifted by a small amount relative to the original flipped map. This doesn’t happen if I save and reopen the map without flipping. Can you please explain what causes this and if it can be avoided? Thanks, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

2 3

Color accuracy in ChimeraX / flat lighting
by Élie Lambert 17 Apr '24

17 Apr '24

Hi all, I wrote a script to color code individual chains of a structure based on fold change values. When I plug the resulting rgb values in ChimeraX, the colors that are rendered are off by quite a bit in some cases. Attached is an example demonstrating such a difference. On the left is shown the color provided for the selected chain, which shows correctly in the 'Select color' window as rgb(196,216,214). However the resulting structure rendered has a different actual color (rgb(227,251,248), as measured with eyedropper tool in Illustrator). This variation is not consistent, colors with higher saturation are not impacted as much, but can still be a bit off. I am using flat lighting with depthcue off, which I believe should mean that no shadows could affect the rendering. I have tried providing colors in other formats such as hex with no difference. I just updated to ChimeraX version 1.7.1 which also did not help (Windows). Please let me know if I am missing anything obvious. Thanks in advance! Regards, Elie

4 5

Re: Dealing with netcdf trajectories
by Enrico Martinez 17 Apr '24

17 Apr '24

Hello Eric, just one question. When I load a netcdf trajectory using: open ./trajectory_part1.nc structureModel #1 Would it be possible to additionally precise the range of the loaded frames e.g. to load the first 5000 frames or in range of 500 to 5000 etc? I also noticed that the maximal number of frames is 9999, isn't it ? Many thanks in advance ! Enrico Il giorno gio 11 apr 2024 alle ore 19:49 Eric Pettersen <pett(a)cgl.ucsf.edu> ha scritto: > Happy to help. :-) > > —Eric > > On Apr 11, 2024, at 12:52 AM, Enrico Martinez via ChimeraX-users < > chimerax-users(a)cgl.ucsf.edu> wrote: > > Thank you very much Eric !! > > Il giorno mer 10 apr 2024 alle ore 18:24 Eric Pettersen <pett(a)cgl.ucsf.edu> > ha scritto: > >> Hi Enrico, >> Add "replace false" to the open command you use when opening the second >> set of coordinates and it will append those coordinate to the current ones. >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> >> On Apr 10, 2024, at 2:34 AM, Enrico Martinez via ChimeraX-users < >> chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Dear Chimera-X users ! >> >> Typically having loaded pdb of the system I use the following command to >> load the netcdf file, which replaces current pdb with the trajectory: >> open ./trajectory_part1.nc structureModel #1 >> >> would it be possible to load in the same section the second part of the >> same trajectory and merge the both into the same ensemble ? >> E.g. if I run subsequently the same command with another trajectory, it >> will produce another ensemble related to the second trajectory (and not >> merge the both together): open ./stripped_*part2.nc structureModel #1 >> >> Many thanks in advance! >> >> Enrico >> _______________________________________________ >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >> Archives: >> https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >> >> >> _______________________________________________ > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu > Archives: > https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ > > >

2 3

Re: ChimeraX download for academic research
by Guillaume Gaullier 17 Apr '24

17 Apr '24

Click on one of the download links for a specific installer (I don't know which operating system you use, but choose the correct one). Only then will you see the license text. And please keep the list in CC when replying. I hope this helps, Guillaume ________________________________ From: Muhammad Tahir <tahirmicrobiologist(a)gmail.com> Sent: Friday, April 12, 2024 9:41:38 AM To: Guillaume Gaullier Subject: Re: [chimerax-users] Re: ChimeraX download for academic research After clicking the link, I did not see the academic link. On Fri, Apr 12, 2024 at 3:39 PM Guillaume Gaullier <guillaume.gaullier(a)kemi.uu.se<mailto:guillaume.gaullier@kemi.uu.se>> wrote: Hello, Did you try clicking on the download link Elaine sent? It takes you to a list of installers, and when you click on one of these download links you will be shown the text of the academic/teaching/personal use license (there is even a button to print it). Cheers, Guillaume ________________________________ From: Muhammad Tahir via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Sent: Friday, April 12, 2024 4:46:45 AM To: ChimeraX Users Help Subject: [chimerax-users] Re: ChimeraX download for academic research Dear Elaine, Thank you for your kind reply. Sorry to say but it did not help me. I need it for academic purposes but I do not have license information. How to get academic/research purpose ChimeraX please On Wed, Apr 10, 2024 at 11:56 PM Elaine Meng <meng(a)cgl.ucsf.edu<mailto:meng@cgl.ucsf.edu>> wrote: See "Download" quick link on the left side of the ChimeraX home page. Here is the ChimeraX home page, the quick links are on the left <https://www.rbvi.ucsf.edu/chimerax/index.html> Or if you still don't see it, the direct link to the download page is <https://www.rbvi.ucsf.edu/chimerax/download.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 10, 2024, at 3:25 AM, Muhammad Tahir via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: > > > Dear management > Have a good day. I did not see the link for subject download please. COuld you help > -- > > Warm Regards: > Dr Muhammad Tahir Khan > PhD Bioinformatics > YOUTH EDITORIAL BOARD MEMBERS > Springer; Interdisciplinary Sciences: Computational Life Sciences > https://www.springer.com/journal/12539/editors > Google Scholar: https://www.springer.com/journal/12539/editors > ORCID ID:https://orcid.org/0000-0003-1158-2133 -- Warm Regards: Dr Muhammad Tahir Khan PhD Bioinformatics YOUTH EDITORIAL BOARD MEMBERS Springer; Interdisciplinary Sciences: Computational Life Sciences https://www.springer.com/journal/12539/editors Google Scholar: https://www.springer.com/journal/12539/editors ORCID ID:https://orcid.org/0000-0003-1158-2133 VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy -- Warm Regards: Dr Muhammad Tahir Khan PhD Bioinformatics YOUTH EDITORIAL BOARD MEMBERS Springer; Interdisciplinary Sciences: Computational Life Sciences https://www.springer.com/journal/12539/editors Google Scholar: https://www.springer.com/journal/12539/editors ORCID ID:https://orcid.org/0000-0003-1158-2133 VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.

4 14

Fwd: Rotating bonds chimeraX
by Eric Pettersen 16 Apr '24

16 Apr '24

> Begin forwarded message: > > From: "Leonardo BETANCURT ANZOLA" <leonardo.betancurt-anzola(a)pasteur.fr> > Subject: Rotating bonds chimeraX > Date: April 16, 2024 at 5:49:03 AM PDT > To: ChimeraX <ChimeraX-bugs-admin(a)cgl.ucsf.edu> > > Hello, > > I was wondering if in ChimeraX it is possible to choose which side of a bond moves and which stays still when using the right mouse feature “bond rotation”. > > Thank you and have a nice Tuesday, > > Leo B. >

2 1

ChimeraX question
by Amita Mohan 16 Apr '24

16 Apr '24

Hello, I would appreciate if you please answer the following questions: 1. I am using chimeraX, and I have a trouble getting results from Alphafold. The Google Colab keep on termination without saving results. Could you please help? 2. I am using hydrogen bond tool, how can I save all the H-bonds in the protein as file containing all the information for the paired residues involved in the H bond. Similarly, I also would like to save the information of residues involved in the protein-protein interactions. I hope to hear from you. Best, Amita Department of Biology University of Pennsylvania

3 4

align the atoms
by 化工化工 16 Apr '24

16 Apr '24

Dear Professor： Hello, I have aligned the atoms #1 of different models with the command "align #1:1 toAtoms #2:1", but I found that the atoms #1 don't overlap very well, which affects the aesthetics of the publication. So, I would like to ask you if there is a way to align the green atoms in the center, thank you very much (see Figure 1)! 化工化工 1366924572(a)qq.com  

2 4

ModuleNotFoundError: No module named 'chimerax'
by Antony Merlin Jose 15 Apr '24

15 Apr '24

Hello, I am a relatively new user of ChimeraX. I would like to be able to run commands on chimerax 'headless' by passing them from python. When I used 'from chimerax.core.commands import run' within the python program, I get the error 'ModuleNotFoundError: No module named 'chimerax''. I am using a MacOS 13.5 and the version of Chimera I have installed is 1.7.1 Any help is much appreciated. Thank you Antony -- Antony M Jose [he/him/his] Associate Professor, Department of Cell Biology & Molecular Genetics, Director, MOCB Concentration Area - Biological Sciences Graduate Program University of Maryland, Rm 2136, Bioscience Research Building, 4066 Campus Drive, College Park, MD - 20742. Website: https://science.umd.edu/cbmg/joselab/

2 1

Download issue for Realsense plugin
by Casey Eubanks 12 Apr '24

12 Apr '24

Hey guys, I am trying to download the realsense plugin for Chimerax but I am getting this error on the download page [cid:image001.png@01DA8CC9.5111D810] Can you help me with this? Thanks, Casey Eubanks Service Desk Specialist MOBILE (205) 617-0581 time zone United States, Central Time Zone (CST) [cid:image002.png@01DA8CC9.5111D810]<https://www.biocryst.com/> "Go Fast, Patients are waiting" If you need immediate IT support please submit a ticket to ITsupport(a)biocryst.com<mailto:ITsupport@biocryst.com> CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

3 3

hide silhouettes for pseudobonds and mesh
by Daniel Larsson 12 Apr '24

12 Apr '24

Hi all, Is it possible to specifically hide silhouettes? The “graphics silhouettes” command unfortunately does not take a spec argument. One example is to hide it for the mesh when you want to show the model and the map at the same time. Silhouettes around the mesh can make the scene look very cluttered. For this particular case, my colleague showed me a trick to use the selection command instead of “graphics silhouettes” and change the appearance of the selection, e.g. “graphics selection color black width 1”. But it gives slighly different apperance with far clip planes, where silhouettes are truncated while selections are enclosing clipped elements, removing some of the depth illusion from the mist. Another scenario is for pseudobonds, e.g. when displaying cartoon and mainchain atoms at the same time using the trick with “cartoon suppress false; cartoon tether opacity 0” given in this thread https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu… I like to have the cartoon visible to guide the eye where the main chain goes, but I do not want the pseudo bonds to be visible since that adds clutter and is confusing. But the silhouettes command will outline the connections to the ribbon for the C3’ and C4’ atoms in nucleic acids. Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

2 3

ChimeraX download for academic research
by Muhammad Tahir 12 Apr '24

12 Apr '24

Dear management Have a good day. I did not see the link for subject download please. COuld you help -- *Warm Regards:* *Dr Muhammad Tahir Khan* *PhD Bioinformatics* *YOUTH EDITORIAL BOARD MEMBERS * *Springer; Interdisciplinary Sciences: Computational Life Sciences* *https://www.springer.com/journal/12539/editors <https://www.springer.com/journal/12539/editors>* *Google Scholar: https://www.springer.com/journal/12539/editors <https://www.springer.com/journal/12539/editors>* *ORCID ID:*https://orcid.org/0000-0003-1158-2133

2 2

chimeraX silhouette look spotty
by kellychen52071＠gmail.com 11 Apr '24

11 Apr '24

Dear ChimeraX support team, I'm experiencing an issue with ChimeraX silhouette showing dark spots. I’m using ChimeraX version 1.7.1. Please see the picture attached. Could you please help me resolve this? I’m using the latest version of macOS Sonoma 14.4.1 (graphics: intel iris plus graphics; processor: 2GHz Quad-core Intel core i5) Is this a graphic issue, this may be a ChimeraX bug for the newest version of mac as my peers who are using an older version of mac do not have this ChimeraX issue.

2 1

chimeraX silhouette show dark spots
by Kelly Chen 11 Apr '24

11 Apr '24

Dear ChimeraX support team, I'm experiencing an issue with ChimeraX silhouette showing dark spots. I’m using ChimeraX version 1.7.1. Please see the picture attached. Could you please help me resolve this? I’m using the latest version of macOS Sonoma 14.4.1 (graphics: intel iris plus graphics; processor: 2GHz Quad-core Intel core i5) Is this a graphic issue? This could be a ChimeraX bug for the newest version of mac as my peers who are using an older version of mac do not have this ChimeraX issue. Thank you for your help, Kelly

1 0

Mesh settings in ChimeraX
by Matthew Hancock 11 Apr '24

11 Apr '24

Hello, I have a density map I am visualizing as a mesh in ChimeraX. If I recall there are settings to manipulate the mesh visualization (line width, antialiasing, etc.) but I cannot them. If they exist, where might I find them? Thank you. Best Matthew

3 2

Dealing with netcdf trajectories
by Enrico Martinez 11 Apr '24

11 Apr '24

Dear Chimera-X users ! Typically having loaded pdb of the system I use the following command to load the netcdf file, which replaces current pdb with the trajectory: open ./trajectory_part1.nc structureModel #1 would it be possible to load in the same section the second part of the same trajectory and merge the both into the same ensemble ? E.g. if I run subsequently the same command with another trajectory, it will produce another ensemble related to the second trajectory (and not merge the both together): open ./stripped_*part2.nc structureModel #1 Many thanks in advance! Enrico

2 2

Not able to sign up to start a thread in RBVI mailing list
by Kelly Chen 10 Apr '24

10 Apr '24

Hi, I signed up using my email address, but I don’t receive an email confirmation in the inbox with steps for finishing an account creation. I checked my spam folder as well. Could you please help me sign up an account? Thank you, Kelly

2 1

Central path for bundles on shared computing environment?
by Ricardo Righetto 09 Apr '24

09 Apr '24

Hi, We are setting up a new cluster at our university, and I stumbled upon the following problem: our nodes used for remote visualization don't have access to the internet. Therefore, users running an interactive graphical session won't be able to install bundles by themselves, which was the case in our old cluster. One workaround is to start ChimeraX either without GUI or with X forwarding over SSH on one of the normal login nodes (no high-end visualization capability) just for the purpose of downloading and installing bundles from the toolshed. This is however inconvenient to most users. Another approach is to install using the 'toolshed' command with a pre-downloaded wheel, but also not ideal. My thought would be to preinstall the most common plugins we use (like ArtiaX and ISOLDE) into a shared location, and ChimeraX would then find the bundles installed there upon startup. Therefore, my question is: is any other path other than the user's home folder supported for installing bundles? If yes, what is the order of search paths? Alternatively, is there some environment variable or other setting that I can use to tell ChimeraX where to find installed bundles? Thanks in advance, -- Ricardo Diogo Righetto

3 3

Morphing Protein/NA Complex
by Shawn Rumrill 09 Apr '24

09 Apr '24

Hello All, I am trying to create an animation morphing between two states of a protein/nucleic acid complex (one binary, one with an incoming nucleotide). Excluding the nucleotide, the corresponding chain IDs between structures are the same and the sequences are the same. In both ChimeraX and PyMol, I am able to create the morphing animation however, only the protein appears (nucleic acid just does not appear in the animation). Am I missing something obvious? I appreciate any insights. Thanks, Shawn R

2 1

Opening chimera within MS powerpoint
by Prathvi Singh 09 Apr '24

09 Apr '24

Hi Elaine, I was wondering whether it it possible (either directly or via a plugin) to open a UCSF chimera/chimeraX window within a Microsoft powerpoint slide so that I can open a PDB file directly within the slide and perform different types of operations (showing distance between 2 atoms which someone from the audience demanded to know, for example)? This way, I would be able to satisfy the doubts of the audience without breaking the flow of the presentation. Thank you, -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

7 10

Transparency of cartoon and surface
by Enrico Martinez 09 Apr '24

09 Apr '24

Dear ChimeraX users, I am trying to add transparency on the cartoon representation of the protein that have additionally transparent surface in the same session. hide protein target a surface protein rainbow protein target c palette paired-12 rainbow protein target s palette paired-12 transparency 90 transparency protein 10 target c The last command hides all cartoons. I've also tried adding the transparency option directly to the rainbow command: rainbow protein target c palette paired-12 transparency 20 But it had the same effect as the total disappearance of the cartoons. Is it possible to have two different levels of the transparency on both cartoon and surface representation ? Thank you in advance ! Enrico

2 2

About surface representation
by Enrico Martinez 08 Apr '24

08 Apr '24

Dear ChimeraX users! I am performing visualization of a molecular dynamics trajectory containing a membrane system. I have two questions about surface representation. 1- I've found that the quality of the surface could be mainly controlled using two options gridSpacing and probeRadius so that decreasing the both usually produces better results. Are there other relevant parameters that could improve the quality of the surface ? 2- Setting different degrees of transparency of different selections. In the case when the lipids in the modelled membrane are splitted into two parts (according to the amber force field) I tried to colour the heads and tails differently setting different degree of transparency, using # first color the entire membrane in blue color ~protein blue surface transparency 40 # color only the headgroups in red setting less transparency color :PC red surface transparency 80 This looks as expected only in the current frame. However, when I start to play a trajectory using coordset, the both selections become equally transparent (setting to 40). Is it possible to control this in a more flexible way ? Thank you very much in advance Best regards Enrico

3 6

Suggestions for optimizing movie quality when working with file size limits?
by Vorländer,Matthias Kopano 08 Apr '24

08 Apr '24

Dear ChimeraX team, Making movies in ChimeraX is my favorite way of communicating my research, but unfortunately many journals have strict file size limits for supplementary movie files (30 MB in my case). I am wondering if there are suggestions for settings that give relatively small files with good visual appearance, i.e a specific format that works better then others. I am currently encoding in .mp4. Is it preferable to set qscale rather than quality/bitrate? I assume both bitrate and the windowsize scale linear with data size? Or are there recommendations for external software that efficiently compresses high-quality ChimeraX movies? Many thanks, Matthias

2 2

How to download prepared molecule as pdb file in chimera X
by Mokshith Dg 07 Apr '24

07 Apr '24

2 2

Visually filtering out unstructured regions
by David S. Fay 06 Apr '24

06 Apr '24

Hi, I was looking for a way to filter out (hide) low scoring pLDDT regions of proteins so my models have less red "spaghetti strands" in my ribbon diagrams. I tried looking in the documentation for a command or pulldown option, but maybe missed it. Thanks in advance! David

3 3

ChimeraX becomes the default HTML viewer on Linux
by Guillaume Gaullier 05 Apr '24

05 Apr '24

Hello, I encountered an annoying behavior of ChimeraX on Rocky Linux 9.3, installed with the RPM package: ChimeraX seems to have declared itself the default application to open local html files. When I need to open an html file in ChimeraX's browser, I do it from within ChimeraX. But when I double-click on an html file, I want it to open in my default web browser (which is already running most of the time, and if not it still starts faster than ChimeraX). I could revert this behavior. I also checked that this doesn't happen on a Mac. If it is intended, in my experience it's been mostly getting in the way when doing tasks unrelated to ChimeraX, so maybe it is worth reconsidering. Cheers, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

2 1

Two-sided surface coloring in ChimeraX?
by Elaine Meng 03 Apr '24

03 Apr '24

> On Mar 31, 2024, at 7:59 PM, Krishnan Raman <RKrishnan(a)BIOCRYST.com> wrote: > > https://www.cgl.ucsf.edu/chimera/ImageGallery/entries/pocket/pocket_2zcp.ht… > Hi Elaine, > How can I mimic this image with chimerax? > Thanks > Krish > > Krishnan Raman > Executive Director, Structural Biology > BioCryst Pharmaceuticals Hi Krish, That Chimera example includes a Chimera command script that uses a "measure contactArea" command with a "slab" option to draw a surface. <https://www.cgl.ucsf.edu/chimera/ImageGallery/entries/pocket/pocket_2zcp.ht…> However, I can't think of a way to do it in ChimeraX, since as far as I know there is no analogous command in ChimeraX currently. ChimeraX has "measure buriedArea" but it does not have an option to create a surface model of just the contact region. Maybe others have ideas? Sorry about that, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

2 1

Re: ChimeraX question
by Tom Goddard 03 Apr '24

03 Apr '24

Hi Amita, Google Colab can predict sequences of about 2000 amino acids with a free google account -- the limit is set by the GPU memory which tends to be 12-16 Gbytes on the old Nvidia GPUs free Google Colab gives you (K8, T4, V100). You can also pay Google Colab to get GPUs with more memory that can handle up to about 5000 amino acids, but such a prediction can take 24 hours and cost about $50. I don't know anything about cosmic2 alphafold. Tom > On Apr 3, 2024, at 11:03 AM, Amita Mohan <amimohan(a)sas.upenn.edu> wrote: > > Is there a limit on amino acid used for prediction? > > Also does cosmic2 alpha fold is different from google Colab alpha fold prediction? > > Best, > > Amita > > > Sent from my iPhone > >> On Apr 3, 2024, at 1:52 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi Amita, >> >> The Google Colab connection will time out if your computer goes to sleep. Google Colab is an interactive service, so if Colab doesn't hear from the web browser window because your computer is sleeping it will disconnect and kill your alphafold prediction. So you may want to turn off sleep on your computer. >> >> Tom >> >> >>> On Apr 3, 2024, at 7:08 AM, Amita Mohan <amimohan(a)sas.upenn.edu> wrote: >>> >>> Thank you Tom for your quick reply. The Colab works but terminate without reaching to the point of downloading results. It shows the connection fails and if I try to reconnect it gives me error message. >>> >>> I do also get response from Elaine. I will work on the recommendation and contact you if I will still have issues. >>> >>> >>> Best, >>> >>> Amita >>> >>>> On Apr 2, 2024, at 4:17 PM, Tom Goddard <goddard(a)sonic.net> wrote: >>>> >>>> Hi Amita, >>>> >>>> You would need to give a more detailed explanation of what you mean by "Google Colab keep on termination". Does Google Colab disconnect? Does an error message from AlphaFold appear? Does it finish and say "Downloading results..."? >>>> >>>> Tom >>>> >>>> >>>>> On Apr 2, 2024, at 12:58 PM, Amita Mohan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>>>> >>>>> Hello, >>>>> >>>>> I would appreciate if you please answer the following questions: >>>>> >>>>> 1. I am using chimeraX, and I have a trouble getting results from Alphafold. The Google Colab keep on termination without saving results. Could you please help? >>>>> >>>>> 2. I am using hydrogen bond tool, how can I save all the H-bonds in the protein as file containing all the information for the paired residues involved in the H bond. Similarly, I also would like to save the information of residues involved in the protein-protein interactions. >>>>> >>>>> I hope to hear from you. >>>>> >>>>> Best, >>>>> >>>>> Amita >>>>> Department of Biology >>>>> University of Pennsylvania >>>>> _______________________________________________ >>>>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>>>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>>>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>>> >>> >>

1 0

Re: ChimeraX question
by Tom Goddard 03 Apr '24

03 Apr '24

Hi Amita, The Google Colab connection will time out if your computer goes to sleep. Google Colab is an interactive service, so if Colab doesn't hear from the web browser window because your computer is sleeping it will disconnect and kill your alphafold prediction. So you may want to turn off sleep on your computer. Tom > On Apr 3, 2024, at 7:08 AM, Amita Mohan <amimohan(a)sas.upenn.edu> wrote: > > Thank you Tom for your quick reply. The Colab works but terminate without reaching to the point of downloading results. It shows the connection fails and if I try to reconnect it gives me error message. > > I do also get response from Elaine. I will work on the recommendation and contact you if I will still have issues. > > > Best, > > Amita > >> On Apr 2, 2024, at 4:17 PM, Tom Goddard <goddard(a)sonic.net> wrote: >> >> Hi Amita, >> >> You would need to give a more detailed explanation of what you mean by "Google Colab keep on termination". Does Google Colab disconnect? Does an error message from AlphaFold appear? Does it finish and say "Downloading results..."? >> >> Tom >> >> >>> On Apr 2, 2024, at 12:58 PM, Amita Mohan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> Hello, >>> >>> I would appreciate if you please answer the following questions: >>> >>> 1. I am using chimeraX, and I have a trouble getting results from Alphafold. The Google Colab keep on termination without saving results. Could you please help? >>> >>> 2. I am using hydrogen bond tool, how can I save all the H-bonds in the protein as file containing all the information for the paired residues involved in the H bond. Similarly, I also would like to save the information of residues involved in the protein-protein interactions. >>> >>> I hope to hear from you. >>> >>> Best, >>> >>> Amita >>> Department of Biology >>> University of Pennsylvania >>> _______________________________________________ >>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >> >

1 0

Missing Vina on ChimeraX
by Luigi Marongiu 03 Apr '24

03 Apr '24

Dear sir or madam, I am using UCSF ChimeraX version 1.5 (2022-11-24). I have been trying to use AutoDock Vina but there is no such command in my version. How do I install it into ChimeraX (as shown in many tutorials, Vina is part of Chimera)? Thank you. Best regards, Luigi Marongiu Ph.D., B.Sc. (Hons.)

4 6

Re: Can α-carbon trace and bond be adjust for PBC?
by qizan chen 02 Apr '24

02 Apr '24

Thanks, I tried to update Eric’s script to do it by my own as attached. It works well for my system.

2 1

About Uninstall
by 김재욱 02 Apr '24

02 Apr '24

Hello. I installed chimera uscf on the server using mobaxterm, and even if I delete all the chima related files after installation, chima uscf will run when using juppter notebook, what can I do?

2 1

question about pb file
by Renee Garza 02 Apr '24

02 Apr '24

Hi there! I've been saving pb files and see that the colors are of varying shades and transparency. I have looked at the link regarding the color key however some colors in the pb files are not in the list. I'm wondering if there's a place to look at the degree of confidence based on color somewhere or a way to have the output with the general color like red, blue, orange, yellow, etc. instead of very specific shades. Thanks, Renee

3 4

Range selection dose not work.
by 洪冉 02 Apr '24

02 Apr '24

Dear Users and Developers of ChimeraX, I am attempting to make a selection of a range of atoms by their numbers in ChimeraX. However, the command I have used does not seem to work in my case. The command in question is sel #1:@1-3. Could anyone assist me with this issue? For screenshots, please see below. Many thanks in advance! Ran

3 3

Can α-carbon trace and bond be adjust for PBC?
by qz.chen＠tamu.edu 02 Apr '24

02 Apr '24

Hi, I want to use ChimeraX to visualize the protein slab simulation in the condensed phase as the link below. Unlike typical protein simulations, simulations of the condensed phase slab often need to keep the atoms inside the box for more accurate visualization. This means that particles between proteins may be jumping, leading to unreasonable lines appearing in the visualization. I have not found a way to adjust this in ChimeraX. https://www.biorxiv.org/content/10.1101/2020.08.05.237008v1.full Is there a way to limit the maximum distance between carbon and bond among particles? Thanks!

3 5

Define axis along z?
by Oliver Clarke 01 Apr '24

01 Apr '24

Hi, For symmetric EM volumes, it would be useful to be able to easily create an axis corresponding to the molecular symmetry axis - generally coincident with a vector parallel to the Z-axis of the box, directly through the center. Is there an easy way to create such an axis in ChimeraX for an arbitrary map? It would be useful to have such an axis in order to rotate a volume around the molecular symmetry axis, even in the absence of a model (this is fairly easy to do if a model is present using define axis). This might be a useful generic extension to "define axis", if there isn't already an easy way to do so. Cheers Oli

3 4

Difficulty with Z-translation - bug?
by Oliver Clarke 01 Apr '24

01 Apr '24

Hi, I can't seem to get the mousemode "Z-translate selected models" to work properly. I have "translate selected" set to Alt+left-drag, so per the docs ("assigned button + Ctrl (in that order) switches to Z-translation instead"), Alt+Ctrl+left-drag should translate the selected model in Z. It does not, or at least in any reproducible manner. Watch the selected yellow marker in the side view here on the right hand side: https://www.dropbox.com/scl/fi/vds0cwu0zizclg64vlxqc/z_translate_bug.mov?rl… 1. Initially I translate in x-y using Alt-drag - works fine. 2. I try to translate in z using alt-ctrl-drag - nothing happens 3. I keep trying translate in z, and eventually it "works" - but if you look closely you will see that the movement of the marker is not synced up with the direction/speed of the mouse cursor. Is this a bug? I remember testing this when it was initially implemented and I thought it worked fine so I suspect so...? Cheers Oli

3 7

*.mdb files from MOE (chemcomp)
by Krishnan Raman 29 Mar '24

29 Mar '24

how to convert docking poses from MOE software to be read into chimerax? thanks Krish CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

3 4

pTM and ipTM Score Access
by Haley V Goodwin 27 Mar '24

27 Mar '24

Hello! I am using ChimeraX to use AlphaFold Multimer. I have read from a couple of places that AF provides pTM and ipTM scores to evaluate the quality of the models. I was wondering how I access these values from ChimeraX. I have looked through the results zip file, but can’t seem to find where these values may be stored. Thank you so much for your help! Best, Haley Goodwin

2 1

Re: isolde write phenixRsrInput (how to restrain ions?)
by Shahid, Taha (Dr.) 27 Mar '24

27 Mar '24

Hi Tristan, That worked perfectly - many thanks for your help! Phenix.metal_coordination didn’t like for_phenix.cif file created by Isolde write phenixRsrInput, but I was able to create the edits file by saving the model file as a PDB from ChimeraX directly. Cheers and happy Easter, Taha On 25 Mar 2024, at 16:15, Tristan Croll <tcroll(a)altoslabs.com> wrote: You don't often get email from tcroll(a)altoslabs.com. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> ***CAUTION:*** This email was sent from an EXTERNAL source. Think before clicking links or opening attachments. Hi Taha, I'm very glad you find ISOLDE useful! Regarding magnesium (and metal ions in general): ISOLDE itself doesn't currently try to write extra Phenix restraints for these, but you can use the program phenix.metal_coordination to generate an edits file that you can add to the phenix.real_space_refine input. That should automatically create a set of bond and angle restraints for all metals in the model. Best, Tristan On Mon, Mar 25, 2024 at 3:46 PM Shahid, Taha (Dr.) via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Dear Tristan, I find ISOLDE invaluable for my work. Not only has it enabled me to build models of the highest quality, but been hugely instructive in giving me an instinctive ‘feel' for protein structure. I am having a minor problem with magnesium ions moving out of density when I run phenix.real_space_refine with settings output by isolde write phenixRsrInput. I typically specify restrainPositions true and includeHydrogens true as well. Is there a way to restrain these ions as well (perhaps an edit I could make to the real_space_refine.eff file)? Many thanks, Taha _______________________________________________ ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT

1 0

change chain description
by Joshua Arribere 27 Mar '24

27 Mar '24

Hello, When I load a pdb into chimerax, a table appears with the chain IDs and associated descriptions. I would like to change the chain descriptions. How do I do that? Thank you, J

3 2

Apple's cpus for trajectory visualisation
by Enrico Martinez 26 Mar '24

26 Mar '24

Dear ChimeraX users ! I wonder about the performance on the modern Apple CPUs: using several Apple's models as a benchmark, I tested Chimera-X on the 2015 and 2017 iMacs equipped with the i7 8 cores and then on the 2023 Macbook Pro equipped with the Apple m2pro chip. In the end, although the modern hardware was much more stable (never mind when loading large netcdf trajectories, as I reported in the case of the 2015 iMAC), I only noticed a slight increase in performance during film editing. As a benchmark, I took a very large model containing the membrane with an embedded oligomer and loaded a trajectory of 5500 frames in Chimera-X. I used surface rendering with 0.4 grid spacing for everything. While everything worked fine, I was able to produce a short 30-second film of 750 frames in about 1h30 on the m2pro, which was almost the same as on my imac 2015. Is there any way to improve the performance of film-making on modern Apple CPUs? Many thanks in advance Enrico

3 6

ChimeraX_question
by 杜博文 26 Mar '24

26 Mar '24

hello,  Chimerax will have an error when we want to use the ribbon inside color white command, please guide me to correct this mistake,Thx. 杜博文南方科技大学/研究生/研究生2021级广东省深圳市南山区学苑大道1088号  

2 1

Re: Chimera X Matchmaker RMSD
by Elaine Meng 25 Mar '24

25 Mar '24

(CC-ing chimerax-users(a)cgl.ucsf.edu since that is the recommended address for ChimeraX questions as long as they do not include private data. Email sent to me directly has more chance of falling through the cracks.) Dear Dr. Sharyn Endow, The Matchmaker algorithm in ChimeraX is the same as in Chimera. So everything I said before about Chimera's Matchmaker is also the case in ChimeraX. If you have the "iteration" option turned on it doesn't use all aligned columns but instead prunes residue pairs for a better fit of the core. If you are showing the sequence alignment, it shows what set of positions were used for the final fit as a light orange colored box. As before, it uses only the CA-CA pairs within those columns, not the side chains. These overall RMSD values are reported in the Log. "pruned" refers only to the fit iteration process, where iteration prunes away some pairs so that they are not used in the final fit. See "Fitting" at the bottom of the "Matchmaker" help: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/matchmaker.html#fitting> Or, if you are using the "matchmaker" or "mmaker" command, see the "cutoffDistance" option for the description of iteration and pruning: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/matchmaker.html#options> If you mean the RMSD header across the top of the sequence alignment, that is a different thing calculated per column (not for the whole structures overall), and you can control in the Sequence Viewer Settings whether this RMSD histogram is calculated CA-only or backbone-only. Neither of them uses the sidechains. If a pairwise alignment, "CA RMSD" boils down to just the CA-CA distance. Simply selecting some range of residues on the sequence alignment doesn't change anything. See help for Sequence Viewer, its header lines, and its Settings: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#headers> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/sequenceviewer.html#settings> Finally as mentioned in my previous answer about Chimera, you can use the "rmsd" command to calculate RMSDs over any sets of atoms that you choose (with or without sidechains) without changing the current positions of the structures. The more tricky part is that you have to specify in the command which atoms to pair with which atoms, since it is not calculated automatically like it is in Matchmaker. The syntax is a little different than in Chimera: there is a "to" between the two sets of atomspecs, and in ChimeraX the slash symbol "/" is used to indicate chains. "rmsd" command <https://rbvi.ucsf.edu/chimerax/docs/user/commands/rmsd.html> ChimeraX atomspec including many examples: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > On Mar 23, 2024, at 8:09 AM, Sharyn Endow, Ph.D. <sharyn.endow(a)duke.edu> wrote: > > Dear Dr Elaine Meng, > > We wrote to you a few years ago regarding Chimera RMSD and you were kind enough to send the information below. We now have a few Q's regarding Chimera X Matchmaker, which displays RMSD values, e.g., when all beta-strands are selected in the Sequence Viewer window. > > • We would like to know what the RMSD values correspond to after aligning two protein sequences using Matchmaker Iwhich uses only only one point per residue for fitting) and selecting all b-strands in the Sequence Viewer window. Is a single RMSD value calculated for each residue to obtain the average RMSD for the "pruned" or all atom pairs and, if so, is the RMSD value between the single point per residue that was used for fitting? > > • Is there some way to obtain the C-alpha RMSD values but not the side chain values, after aligning two protein chains in Matchmaker in Chimera X? > > • What does "pruned" atom pairs mean in this context? > > T > hank you in advance for your help - > > Sincerely, > > Sharyn A. Endow, PhD > Professor of Cell Biology, DUMC > DUS, Cell Biology > PO Box 3709 / 245/247 Sands Bldg / 303 Research Drive > Durham, NC 27710 USA T 919 684-4311 F 919 681-9929 > > > > From: Elaine Meng <meng(a)cgl.ucsf.edu> > Date: January 25, 2021 at 4:26:34 PM EST > To: "Sharyn Endow, Ph.D." <sharyn.endow(a)duke.edu> > Cc: Chimera <chimera-users(a)cgl.ucsf.edu> > Subject: Chimera RMSD > Reply-To: Chimera <chimera-users(a)cgl.ucsf.edu> > > > From: "Sharyn Endow, Ph.D." <sharyn.endow(a)duke.edu> > Subject: Chimera RMSD > Date: January 23, 2021 at 11:27:17 AM PST > > Thank you for your work in developing Chimera. We are trying to use Chimera RMSD to quantitate twisting of a beta-sheet and would like to know what the syntax is to list rmsd values for specified residues corresponding to a beta-strand, not just for single residues. Is it possible to list these values using RMSD? If so, we would greatly appreciate knowing how to get started. > > Sincerely, > Sharyn > > Hi Sharyn, > You can specify any sets of atoms/residues that you like in the RMSD command, as long as there are equal numbers of atoms in the two sets that you specify (from two different models). They will be paired in the order specified. We have a command-line "atom specification" syntax for that kind of thing. There is a longish page with lots of examples here: > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html > > > In your case, you may need to specify residue numbers, chain ID, and possibly atom names if you just want to use alpha-carbons or backbone as opposed to all atoms of the residues. E.g. something like > > rmsd #0:12.A,57-63.A #1:14.A,59-65.A > > ... for all atoms of model 0 residues 12 and 57-63 in chain A vs. all atoms of model 1 residues 14 and 59-65 in chain A. Or to use CA-only or backbone only: > > rmsd #0:12.A,57-63.A@ca #1:14.A,59-65.A@ca > rmsd #0:12.A,57-63.A@n,ca,c,o #1:14.A,59-65.A@n,ca,c,o > > Of course the numbers could be the same in the two models, I just was trying to give a more general example. > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > P.S. the chimera-users(a)cgl.ucsf.edu address CC'd here is recommended for general Chimera how-to or is-it-possible types of questions

2 4

isolde write phenixRsrInput (how to restrain ions?)
by Shahid, Taha (Dr.) 25 Mar '24

25 Mar '24

Dear Tristan, I find ISOLDE invaluable for my work. Not only has it enabled me to build models of the highest quality, but been hugely instructive in giving me an instinctive ‘feel' for protein structure. I am having a minor problem with magnesium ions moving out of density when I run phenix.real_space_refine with settings output by isolde write phenixRsrInput. I typically specify restrainPositions true and includeHydrogens true as well. Is there a way to restrain these ions as well (perhaps an edit I could make to the real_space_refine.eff file)? Many thanks, Taha

2 1

ISOLDE query - non crystallographic symmetry?
by Oliver Clarke 25 Mar '24

25 Mar '24

Hi Tristan, I've been using the latest version of ISOLDE with ChimeraX 1.7.1 and it is working beautifully - very smooth simulation and very helpful for fixing up problem areas! One query - is there any support for non crystallographic symmetry in ISOLDE, or if not is this on the roadmap? Thinking both in terms of NCS restraints, but also in terms of propagating edits from one subunit of an oligomer to all the others - this would be very helpful to have for a lot of folks I think, as so many proteins are oligomeric. Thanks for the wonderful piece of software! Cheers Oli

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Difficulty unsubscribing
by BARRY E DEZONIA 25 Mar '24

25 Mar '24

I am trying to leave this email list and currently am unable to. I send email to: chimerax-users-leave(a)cgl.ucsf.edu And it processes and says my email barry.dezonia(a)wisc.edu is not a list member. That is because I signed up with bdezonia(a)wisc.edu.. My mail service treats them as equivalent but it only sends out on the incorrect email address. Can someone unsubscribe ndezonia(a)wisc.edu? I can't figure out how to get my email client to use my other email address as the sending address.

1 0

Adding lipid bilayers to chimerax movie
by Kevin Felt 25 Mar '24

25 Mar '24

Hello ChimeraX Users, I'm trying to make a movie in chimerax involving a membrane protein, and I would like to have some representation of where the inner and outer lipid bilayer leaflets are relative to the protein transmembrane region, ideally represented as phospholipids. Is it possible to do this within Chimerax? I've thought about encoding the movie to mp4 and then figuring out how to simply overlay a bilayer image onto the mp4 where I want with some other software , but I foresee resolution and scaling issues when doing that. Thank you! Sincerely, -- Kevin C. Felt PhD Candidate - Chakrapani Lab Department of Physiology and Biophysics School of Medicine Case Western Reserve University

2 2

Color a surface by seq_conservation of neighboring residues
by Esser, Lothar (NIH/NCI) [E] 22 Mar '24

22 Mar '24

Hi, my intention is to make a figure that maps the degree of sequence conservation of surrounding residues onto a surface drawn over the said inhibitor. I know I can color surfaces by distances and other parameters but I could not find out how to color a surface by properties of neighboring residues or atoms. Is there perhaps a way to convert an atom attribute like conservation into a map that then could be used to color a surface? Alternatively, I thought I could write out the calculated sequence conservation as a pdb file with say the b-factor column representing the sequence conservation. Unfortunately, that does not seem to be the case. Can you write atom attributes in any other way? - perhaps I missed that. If I had access to the sequence conservation values, I could copy them to the b-factor column of the inhibitor and color its surface by bfactor. Thanks for any advice. Lothar NIH

2 4

Visualisation of distances
by Enrico Martinez 21 Mar '24

21 Mar '24

Dear ChimeraX users ! I need to draw several distance vectors on the 3D structure. Could you provide me with an example of the commands that could automatically draw the distances between two selected atoms with some basic labels on it ? Many thanks in advance Enrico

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Re: Trying to join two structures unsuccessfully
by Maja Divjak 18 Mar '24

18 Mar '24

Alternatively, I guess I could just cut this disordered domain into fragments, move them around and the rejoin them.... -----Original Message----- From: Maja Divjak Sent: Tuesday, 5 March 2024 11:44 AM To: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: RE: [chimerax-users] Trying to join two structures unsuccessfully Dear Elaine, No worries at all, I have received multiple replies, so it is working! Thank you for your response below. Basically, it seems what I'd like to do can't really be done in this way. In another conversation, someone mentioned the tug command. Could this yield what I'm hoping for please? The two ends I'm trying to join are indeed in separate models, so I tried the following command: tug #16/a:345-355 toAtoms #18/A:345-355 which gave the following error: For 0 tugged atoms expected 0 destination atoms, got 84 Would this be the correct approach (I've clearly got the syntax wrong) or is there really no way to do this in Chimera X? Thanks so much and best wishes, Maja PS. How do I join the member's list please? -----Original Message----- From: Elaine Meng <meng(a)cgl.ucsf.edu> Sent: Tuesday, 5 March 2024 11:33 AM To: Maja Divjak <Maja.Divjak(a)petermac.org> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] Trying to join two structures unsuccessfully ! EXTERNAL EMAIL: Think before you click. If suspicious send to CyberReport(a)petermac.org Dear Maja, Apologies if you are getting multiple copies of this answer from me. I keep getting error messages that my reply could not be sent to the list! So, here is my third try. If you've been getting my previous messages (even though I don't think the rest of the list is), please ignore and pardon me for the spam! Adding a bond only works when the atoms are in the same model as each other (typically a structure opened from one PDB file is one model). Also simply adding a bond won't move anything. It will just make a long bond between the atoms in their current positions, or if you choose "reasonable" only, it won't add any bond because the bond would be too long to be reasonable. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds> You can see what model(s) you have by looking in the Model Panel: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/modelpanel.html> If the two atoms are in two different models (typically opened from two different input files), the "join models" Peptide Bond option should work if you really have exactly two atoms selected, the peptide terminal "N" in one model and the peptide terminal "C" in the other model. As far as I can tell these two are selected in your image, so I couldn't say why you get an error message. If the atoms are in the same model as each other, however, it will not work. You would need to split the model so that they are in separate models first. You can try command "info atoms sel" to list in the Log what you have selected. In my "join peptide" test case I get the following, which confirms I have the correct atoms from two different models selected: info atoms sel atom id #1/A:29@C idatm_type Cac atom id #2/A:1@N idatm_type N3+ However, join models is not going to change the conformation of the peptide, it will just move one model (e.g. the entire green one if it has more atoms than the purple one) as a rigid body to form the specified bond with the other model. <https://rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

2 6

How to change transparency of ladder mode of nucleic acids
by Yan ZHANG 张艳 15 Mar '24

15 Mar '24

Dear ChimeraX Team, I hope this email finds you well. My name is Zhang Yan, and I am a beginner of ChimeraX. I am writing to seek assistance regarding how to change transparency of ladder mode of nucleic acids in ChimeraX. Despite trying the command 'trans #1 60 all', I have been unable to achieve the desired effect. Could you please suggest an alternative solution or provide guidance on how to accomplish this task? Thank you for your attention to this matter. Best regards, Zhang Yan

2 3

Is the site down ?
by Marie PREVOST 15 Mar '24

15 Mar '24

Hello, I would like to install ChimeraX on my new laptop but the site seems to be down… Do you know if there are other option to download the installer ? Thank you for your help Best wishes ------- Marie Prevost, PhD Pierre-Jean Corringer’s lab ( site<https://research.pasteur.fr/en/member/marie-prevost/> ) Channel-Receptors Unit Institut Pasteur 25 rue du Dr Roux 75015 PARIS France +33 (0)1 53 55 15 06 (via Teams)

2 2

Question about interpreting variable ipTM scores
by David S. Fay 15 Mar '24

15 Mar '24

Hi, This question isn’t specifically about chimerax, but I hope it’s in the ball park. For most of the protein pairs I’ve tested using multimer, the ipTM scores for the 5-10 models are relatively consistent. For example all 0.2–0.3, or 0.75–0.85, or 0.4–0.6. But occasionally I’ll get one or two very high scores (>0.7) with the rest being low or somewhat randomly scattered. My instinct, of course, is to put more faith in scores when the models converge. At the same time, I don’t want ignore a potentially real interaction. So, I’m wondering how people interpret ipTMs when the numbers are variable between models. What is the reason that some protein pairs show this pattern? Is the good score(s) indicative or something real or a false positive. Are the bad scores indicative of true or false negative? Any thoughts, insights, and possible follow up approaches would be greatly appreciated! David

3 2

Downloading chimera
by Pincus, Seth 15 Mar '24

15 Mar '24

When I try to download Chimera (or connect to any Chimera site), I get the attached error message saying that “www.cgl.ucsf.edu has refused the connection”. I am running Chrome version 122 on a Mac Powerbook running OS12.7.1. My computer is owned by Montana State University and may have some additional security is installed. But I could find nothing in Chrome’s settings that would allow me to connect. Please respond bydirect e-mail, since I cannot get to the site to join the mailing list. Thank you, Seth Pincus, M.D. Professor Department of Chemistry and Biochemistry WWAMI Medical Program Montana State University Bozeman, MT 59717

2 1

only make selection highlighted
by 张楠 14 Mar '24

14 Mar '24

Dear developers, How does chimerax make the stick I selected highlighted and the carton in other areas blurred? I tried to click on view selected, but that only makes the back of the structure blur, not the front. May I ask how to operate to achieve the effect in the picture, only highlight stick？ Looking forward to your answer, thank you！ Best regards, Nan 张楠 zhangnan(a)nankai.edu.cn

2 2

Isolde can't be installed inside ChimeraX 1.5
by Jun Zhang 13 Mar '24

13 Mar '24

Hi ChimeraX, I met an issue when I try to install Isolde inside ChimeraX 1.5. It will stuck there forever. May I ask you if there are any ways to solve this issue? I tried to use website to download the whl file, but it can’t be recongized by ChimeraX. May I ask you for some suggestions if possible? Many thanks in advance and have a nice day! Best regards, Jun Zhang

3 3

a bug with saving Chimera-X session
by Enrico Martinez 13 Mar '24

13 Mar '24

Dear Chimera-X users! I got the following error on my iMAC equipped with Intel CPU after an attempt to save a Chimera-x (ver 1.71) session containing a loaded netcdf trajectory with 7500 frames (with the same system containing only 5000 frames, ain't no problems !!). Yours with thanks Enrico Traceback (most recent call last): File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127, in <lambda> lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output file", ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog _dlg.display(session, **kw) File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 62, in display run(session, cmd) File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 86, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 101, in provider_save saver_info.save(session, path, **provider_kw) File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 95, in save return cxs_save(session, path, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 912, in save session.save(output, version=version, include_maps=include_maps) File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 641, in save fserialize(stream, data) File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py", line 76, in msgpack_serialize stream.write(packer.pack(obj)) ^^^^^^^^^^^^^^^^ File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 285, in msgpack._cmsgpack.Packer._pack File "stringsource", line 67, in cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap File "src/_serialize.pyx", line 253, in chimerax.core._serialize._encode_ext File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 264, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 285, in msgpack._cmsgpack.Packer._pack File "stringsource", line 67, in cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap File "src/_serialize.pyx", line 226, in chimerax.core._serialize._encode_ext File "msgpack/_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack File "msgpack/_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack ValueError: bytes object is too large ValueError: bytes object is too large File "msgpack/_packer.pyx", line 202, in msgpack._cmsgpack.Packer._pack *See log for complete Python traceback.*

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Problem Installing ChimeraX
by Stephen P. Molnar 12 Mar '24

12 Mar '24

I am running Debian-12.6.0 and have encountered a problem installing ChimeraX.flatpak: error: The application edu.ucsf.rbvi.ChimeraX/x86_64/master requires the runtime org.freedesktop.Platform/x86_64/22.08 which was not found The installation was necessitated due to a system crash. Please advise. Thanks in advance. -- Stephen P. Molnar, Ph.D. https://insilicochemistry.net (614)312-7528 (c) Skype: smolnar1

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Re: Difficulty with Z-translation - bug?
by Elaine Meng 11 Mar '24

11 Mar '24

I don't know if that is really true.... it's just that it is what I experienced this morning, and I am extremely uncoordinated... I have to turn off the multitouch actions, for example, because I just can't deal with them personally. Tom G would have to confirm if that's actually in the code before I would want to immortalize it in writing! The current documentation is what was explained to me, although it's possible I misunderstood. Elaine > On Mar 11, 2024, at 9:58 AM, Oliver Clarke <olibclarke(a)gmail.com> wrote: > > Ah I see - the modifier absolutely has to be added after starting an ongoing XY-translation... that is a bit of a pain if you just want to translate something in Z (e.g when moving something with respect to a density map). > > It might be worth making both limitations (initiating from an ongoing XY translation and vertical mouse movement only) a bit more explicit in the help page - it states that the order of the keys is important, but it doesn't really say that you need to start translating in XY before trying it in Z (or at least that wasn't my read of it). Thanks Elaine I think I get it now, very helpful! > > Cheers > Oli >> On Mar 11, 2024, at 12:51 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >> >> Hi Oli, >> Sorry I meant include this info in your bug report, not necessarily to the email list (athough that's fine too)! I won't be the one looking at the bug report, and it might not be addressed right away, so it's good to put the information there. >> >> If by "move models" button you mean the icon for mousmode "translation": >> >> I got a selection box at first and then after I did an XY-translation, being very careful about adding the Ctrl to an ongoing drag, I got Z-translation. >> >> Elaine >> >>> On Mar 11, 2024, at 9:46 AM, Oliver Clarke <olibclarke(a)gmail.com> wrote: >>> >>> I'm on a MBP with M2-Max chip and running Sonoma (14.1). >>> >>> If I activate move models for right-mouse using the GUI "move models" button, then adding a ctrl modifier does not translate in Z, I just get a selection box even with Ctrl-right-drag - same is true if I activate translation from the GUI. >>> >>> Cheers >>> Oli >>> >>>> On Mar 11, 2024, at 12:41 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>>> >>>> I'm on a Macbook Pro with M1 chip running Monterey 12.7.3. I guess we would also be interested whether the Z-translation works with the regular "translation" mode in your situation, as it did for me in my tests this morning. You would also need to use the ChimeraX 1.7 release or newer, of course, since Z-translation wasn't added until last September, according to the Change Log: >>>> >>>> https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog >>>> >>>> Elaine >>>> >>>>> On Mar 11, 2024, at 9:18 AM, Oliver Clarke <olibclarke(a)gmail.com> wrote: >>>>> >>>>> Hi Elaine, >>>>> >>>>> Thanks for the explanation! Yes I am on a mac using a trackpad. I did explicitly assign it (mousemode alt left "translate selected models"). It still doesn't work reproducibly for me (in either daily or stable build), even with vertical motion and after translating in X-Y first... I will report it as a bug, thanks! >>>>> >>>>> Cheers >>>>> Oli >>>>>> On Mar 11, 2024, at 12:00 PM, Elaine Meng <meng(a)cgl.ucsf.edu> wrote: >>>>>> >>>>>> Hi Oli, >>>>>> Short answer is that (at least in my hands) the horizontal motions don't elicit much Z-translation -- try moving the cursor vertically. In all my tests below that worked with translation assignment +Ctrl to give Z-translation. >>>>>> >>>>>> Long answer with several rounds of testing: >>>>>> >>>>>> I don't know if this applies to you, but since I work on a Mac with a trackpad most of the time, I avoid explicitly assigning anything to alt-left or command-left because these emulate the middle and right mouse buttons. >>>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#touchpad> >>>>>> >>>>>> I don't know whether you actually assigned alt-left to translate, but the factory default assignment for middle mouse ( = alt-left if you call trackpad click-drag "left") is translation, so it's effectively the same as what you said. >>>>>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/ui.html#mousemode> >>>>>> >>>>>> Using the factory defaults (translation nominally assigned to middle mouse), the Z-translation with alt-left-drag-Ctrl is working for me on a Mac with trackpad and UCSF ChimeraX version 1.7.1 (2024-01-23) as well as recent daily build 1.8.dev202403072314 (2024-03-07). >>>>>> >>>>>> Next I tried it with two models open, one selected, and the "translate selected models" assigned to right mouse button (= Mac trackpad command-left) and it works fine to XY- and Z-translate (with added Ctrl) the selected model only. >>>>>> >>>>>> If I actually assign >>>>>> >>>>>> mousemode alt left "translated selected models" >>>>>> >>>>>> That also works alt-left to XY translate and Z-translate (with added Ctrl) the selected model only. >>>>>> >>>>>> However, I usually have to try a little XY-translation first before attempting Z-translation because it is a little persnickety and/or I am not coordinated enough to use these multiple keys at the same time. And again, I don't know what exactly is going on in the video you sent, but, horizontal cursor motion doesn't seem to do much Z-translation for rme, only vertical. >>>>>> >>>>>> If you can't get it to work, please use Help.. Report a Bug so we will know your exact version and platform details. >>>>>> >>>>>> I hope this helps, >>>>>> Elaine >>>>>> ----- >>>>>> Elaine C. Meng, Ph.D. >>>>>> UCSF Chimera(X) team >>>>>> Resource for Biocomputing, Visualization, and Informatics >>>>>> Department of Pharmaceutical Chemistry >>>>>> University of California, San Francisco >>>>>> >>>>>>> On Mar 11, 2024, at 7:33 AM, Oliver Clarke via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> I can't seem to get the mousemode "Z-translate selected models" to work properly. I have "translate selected" set to Alt+left-drag, so per the docs ("assigned button + Ctrl (in that order) switches to Z-translation instead"), Alt+Ctrl+left-drag should translate the selected model in Z. It does not, or at least in any reproducible manner. >>>>>>> >>>>>>> Watch the selected yellow marker in the side view here on the right hand side: >>>>>>> >>>>>>> https://www.dropbox.com/scl/fi/vds0cwu0zizclg64vlxqc/z_translate_bug.mov?rl… >>>>>>> >>>>>>> 1. Initially I translate in x-y using Alt-drag - works fine. >>>>>>> 2. I try to translate in z using alt-ctrl-drag - nothing happens >>>>>>> 3. I keep trying translate in z, and eventually it "works" - but if you look closely you will see that the movement of the marker is not synced up with the direction/speed of the mouse cursor. >>>>>>> >>>>>>> Is this a bug? I remember testing this when it was initially implemented and I thought it worked fine so I suspect so...? >>>>>>> >>>>>>> Cheers >>>>>>> Oli >>>>>> >>>>> >>>>> >>>> >>> >>> >> >

1 1

Enclose volume within radius?
by Oliver Clarke 10 Mar '24

10 Mar '24

Hi ChimeraX-ers, Finding an equivalent contour level for 3D classes in cryoEM can be challenging, particularly if the density histograms are sufficiently different that setting a single level does not suffice (and particularly when comparing many classes from a large classification). The options "enclosevolume" and "fastenclosevolume" for the "volume" command are very useful for this (e.g. "volume #* fastenclosevolume 200000"), but fail in the presence of compositional heterogeneity (if there is more ordered stuff in one class and the volume is fixed, the contours will no longer be equivalent). To address this, would it be possible to add a "within_radius" modifier for the "volume fastenclosevolume" command? This would mean one could then set a fixed volume to be enclosed by the contour within a set radius of either the center of rotation, or of an atom selection, making the contour levels at least locally equivalent (which is often what one wants for the purposes of comparison). Cheers Oli

3 4

Notepad or info dialog in ChimeraX?
by Oliver Clarke 08 Mar '24

08 Mar '24

Hi, Is there a command in ChimeraX to launch a notepad? Or to display some text? I would like to make a button that will launch a little window with some info about shortcuts and the like. In Chimera, there was a notepad (the contents of which could be saved with a session) - does something similar, or some kind of custom info dialog, exist in ChimeraX? Cheers Oli

3 3

Question about accreditation
by Enrico Martinez 08 Mar '24

08 Mar '24

Dear ChimeraX users ! I am wondering if I am obligated to mention the name of the ChimeraX software if I use it to creat a cool image and post it to any social media like Facebook or Instagram ?? Or alternatively on the personal web page ? Obviously it could be obligatory for a scientific publication but what s about usage in fully artistic context ?? Many thanks in advance ! Yours sincerely Enrico

2 4

Loading multi-frame pdb using open command
by Enrico Martinez 08 Mar '24

08 Mar '24

Dear Chimera-X users! I have a question regarding the handling of a trajectory saved in multiple-pdb format. Loading such ensemble using dedicated open command typically load all frames at once: open ./my_trajectory.pdb coordset true Would it be possible to specify the range of the loaded frames to reduce the time for data loading e.g. i) to load first 3000 frames or ii) to load from 50 to 5000 frames? Many thanks in advance ! Best wishes, Enrico

3 6

Trying to join two structures unsuccessfully
by Maja Divjak 07 Mar '24

07 Mar '24

Hi there, Hope you're well. I am trying to join the two structures as shown in the image attached. I would like to join the disordered chain shown in green to the purple chain and the residues I would like to join are highlighted. I would like the green disordered chain to be dragged over to join the purple structure without moving any of the ordered domains that are linked to it (orange). I have tried selecting individual atoms ie N and C atoms from these residues (as shown) and using the command tools > structure editing > build structure > join models from the drop down menu. I adjusted C-N length to 1.6 and set to 'move atoms in larger model', thinking this would move the green chain. Hitting apply gives me the error dialogue 'No atoms selected'. I also tried Adjust Bonds > with options for Delete selected bonds > and add reasonable. There are no error messages, but the log says that no bonds were created. Not sure what I'm doing wrong or what the correct process is for joining models in this way please? Is this even possible? Clearly I'm not selecting the atoms appropriately. I am using Chimera X version 1.6.1 Thanks so much and best wishes, Maja Dr Maja Divjak BAppSc(Hons), PhD, Grad Cert 3D Animation (AFTRS) Biomedical Animator Office of Cancer Research [Description: cid:image001.jpg@01D35ECE.31407C60]

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ISOLDE: unable to work with map after selecting another model
by Alexis Rohou 06 Mar '24

06 Mar '24

Hi Tristan, ISOLDE users, Sometimes it's useful to create a new model (e.g. by merging the model of the protein you've been working on with an initial model of the ligand) and then continue working with this new model in ISOLDE. For me, this leads to trouble. Specifically, here's what I do: - start ChimeraX - open a PDB and a map - start ISOLDE - select the PDB model in the "Working on" dropdown - select the map in the "From loaded volume" dropdown - do some simulations until I'm happy with the protein - open a PDB of the ligand - combine the ligand model with the protein model - select the combination model in the "Working on" dropdown - press "start simulation"... get warning "about to start simulation with no map" - press Cancel - check the "From loaded volume" dropdown - it's not possible to select the already-loaded map, which is in the initial "Data manager" Is this intended behavior? I was hoping to be able to continue working against the same map. Cheers, Alexis

2 2

Silhouettes only on selected models
by Pedro Bule 06 Mar '24

06 Mar '24

Hi, I'm writing to know if there is a way to turn on the silhouette graphical option only on selected models in ChimeraX, or is it just a global option? I have a model of an enzyme with its ligand and another model with the electron density loaded from a .map file. I want to display the electron density around the ligand as a slightly transparent mesh without silhouettes (see below) while still having silhouettes on the enzyme and ligand. Is there a way to do this? The silhouettes on the mesh make it too dark and dense (see image 2). Thank you very much Pedro Bule [image: image.png] [image: image.png] -- *Pedro Bule* *Assistant Professor* GLYCOBIOLOGY AND STRUCTURAL ENZYMOLOGY LAB *P:* (+351) 21 365 28 84 // 431379 | pedrobule(a)fmv.ulisboa.pt <email(a)fmv.ulisboa.pt> *Centro de Investigação Interdisciplinar em Sanidade Animal* Faculdade de Medicina Veterinária Av. Universidade Técnica | 1300-477 Lisboa | PORTUGAL

3 2

Connection to GPU
by Minu Chaudhuri 06 Mar '24

06 Mar '24

Hello, I am trying to build a multimeric structure using AlphaFold collab, but it is not connecting to the GPU. How can I get a connection? Is there a fee for this? How to pay for this? Thanks for your help. Minu Chaudhuri, Ph.D. Meharry Medical College Nashville TN 37208 USA

3 2

need Section 508 compliance statement
by Weiss, Carol 06 Mar '24

06 Mar '24

Hello, I would like to use ChimeraX, but the FDA IT administrators will not download the Chimera X software without a statement about its Section 508 compliance for users. Would you please send me available Section 508 compliance information for this software? Thank you, Carol Weiss

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Improvement suggestion: single letter code for swap
by Vorländer,Matthias Kopano 06 Mar '24

06 Mar '24

Dear ChimeraX team, A small feature request: It would be helpful if the swapaa command could accept the single letter code for amino acids as well as the three letter code. This makes it easy to quickly fix a sequence, i.e based on a sequence that is open in the sequence viewer. Many thanks, Matthias

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Mainchain and sideonly atom names
by Sabrina Moffit 05 Mar '24

05 Mar '24

Dear ChimeraX team, So far I've found that these are the atom names classified as mainchain atoms by ChimeraX: ['H3', 'HA2', 'H2', 'CA', 'H', 'H1', 'HA', 'C', 'O', 'HA3', 'OXT', 'N'], by using such command: sel #1 & mainchain; info atoms sel. I'm not sure if there are more atom names classified as mainchain atoms by ChimeraX. Could you please provide me with a comprehensive list of all the atom names of the mainchain atoms (and sideonly atoms as well, if possible) of all types of amino acids? Thank you.

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Conctac map in ChimeraX?
by PABLO HERRERA NIETO 05 Mar '24

05 Mar '24

Hi everyone, I started using chimera after some years. In the new ChimeraX I could not find an option to calculate contact/distances heatmaps for proteins or protein complexes. Is that old funcionality gone for good? However, to check AlphaFold's pLLDT there is a really nice intereactive chart. Is there any option/hack to use that to visualize contacts/distances for any structure? Thanks Pablo -- Pablo Herrera Nieto Dpto. de Estructura de Macromoléculas, lab 15 Centro Nacional de Biotecnología - CSIC

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movie record / encode
by Enrico Martinez 05 Mar '24

05 Mar '24

Dear ChimeraX users! I noticed that there is some difference in the quality of the molecular movies produced in Ubuntu or MacOSX environments. Are there some tricks to improve the quality of the animation produced on ubuntu ? Here are the commands which produced the best results: movie record size 1920,1080 supersample 4 movie encode format h264 quality higher bitrate 25000 how could I modify / add something more with the aim to obtain the best molecular animations ?? Yours sincerely Enrico

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Question
by 张楠 05 Mar '24

05 Mar '24

Dear developers, I have a question I'd like to ask. The structure after refinement appears as helices when opened in PyMOL, but in ChimeraX, it doesn't display as helices, as shown in the figures. What could be the reason for this? Is there a way to make it display as helices in ChimeraX? Looking forward to your answer, thank you！ Best regards, Nan 张楠 zhangnan(a)nankai.edu.cn

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Inquiry - UCSF ChimeraX
by Fumi JINUSHI 05 Mar '24

05 Mar '24

Dear Sirs, We are a sales agent and a custom made computer manufacture in Japan. We focus on R&D sector as a key business area and help researchers and engineers in universities, research institutes and large companies, and provide them with a good selection of industrial products. I wonder if we can sell UCSF ChimeraX and provide our customers with the software installed on our custom made computers. We look forward to your reply. Thank you ! Kind regards, Fumi +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ Fumi JINUSHI web_delivery(a)tegara.com Tegara Corporation 211-17, Higashimikata-cho, Chuo-ku Hamamatsu-shi, Shizuoka, 433-8104 Japan T +81-53-543-6691 F +81-53-543-6689 UNIPOS https://en.tegara.com/service/unipos/ TEGSYS https://en.tegara.com/service/tegsys/ +-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

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right-mouse clipping
by Daniel Larsson 01 Mar '24

01 Mar '24

Hi all, I have some question and comments regarding the very useful right-mouse Clipping tools. I feel they are poorly documented (or documentation is very difficult to find by Google searching). For the Clip tool, it took me forever to realize how to “undo” the clipping (click again). The Zone clipping is a very nice feature, which shows atoms, residue labels and volume inside of an approximately 10 Å sphere and hides the volume and only show cartoon outside of the sphere. Right-clicking on the background hides the labels. Some questions 1. How do I change the back/far clipping plane using the Clip tool (the icon suggests that you can clip into a slab)? 2. If so, is it possible to set a default thickness of that slab? 3. Is it possible to change the radius of the Zone clipping tool? 4. Is it possible to disable the cartoon outside of the sphere of the Zone clipping tool? 5. Alternatively have the ability to have an extra front clipping plane, which “intelligently” follows the camera when zooming in (hiding things closer to the centered region when zoomed in more)? 6. I use the mouse mode to center the view and camera pivot point (mousemode middleMode "center or translate"). It is possible to make the Zone clipping tool also center the view + pivot point so that I don’t have to also middle-click every time? Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Isolde add nucleotide?
by Vorländer,Matthias Kopano 01 Mar '24

01 Mar '24

Dear all, Is it possible to add nucleotides to existing chains, similar to Isolde add aa? Many thanks, Matthias

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Re: Seeking Assistance with PyCharm Debugging Configuration
by Zachary Pearson 28 Feb '24

28 Feb '24

Hi Himal, I'm confused by a couple of things. First, your system packages should list all of ChimeraX's packages, like the screenshot attached to this email. Did you build ChimeraX (make build-from-scratch) and subsequently use ChimeraX's internal Python, not your system Python, to make your virtual environment? Second, the path to your interpreter looks like it's a path to a virtual environment inside ChimeraX itself. In /the base directory of the git repository:/ ./ChimeraX.app/bin/python.exe -m venv .venv --system-site-packages Then in PyCharm -> Settings -> Project: ChimeraX -> Python Interpreter Add a new interpreter path/to/ChimeraX/.venv/Scripts/python.exe Use that as the interpreter for your run or debug configuration. -- Zach On 2/27/2024 1:36 PM, Eric Pettersen wrote: > Nudge, nudge... :-) > >> Begin forwarded message: >> >> *From: *Himal Godage <himalgodage2759(a)gmail.com> >> *Subject: **Re: [chimerax-users] Seeking Assistance with PyCharm >> Debugging Configuration* >> *Date: *February 20, 2024 at 11:34:54 PM PST >> *To: *pett(a)cgl.ucsf.edu >> *Cc: *chimerax-users(a)cgl.ucsf.edu >> >> Hi Eric, >> Thank you for the reply and I appreciate your assistance. >> >> I've been using the internal Python to create a virtual environment >> in my project’s folder, and I've set the Python interpreter path as >> outlined in the documentation. The first attached screenshot is my >> interpreter configuration. >> >> However, my current challenge lies in the debugging section. I've >> created a new Run/Debug Configuration(third attachment) following the >> instructions , as shown in the second attached screenshot. >> Regrettably, when attempting to run the configuration, I encountered >> an error in the console: "No module named chimerax.core" (refer to >> the fourth attached screenshot). >> >> I believe that the issue is regarding a module named chimerax.core >> which I couldn’t find on the project. >> Thank you in advance for your help. >> >> Himal >> >> On Wed, Feb 21, 2024 at 12:39 AM Eric Pettersen <pett(a)cgl.ucsf.edu> >> wrote: >> >> Hi Himal, >> The person on our team that uses PyCharm and that wrote >> that documentation is on a trip to NIH this week and may not be >> able to respond promptly. Reading that page myself, it seems >> that the Debugging section assumes that you set up a virtual >> environment as outlined in the preceding "IDEs" section. Did you >> do that? >> >> --Eric >> >> Eric Pettersen >> UCSF Computer Graphics Lab >> >> >> > On Feb 19, 2024, at 9:40 PM, himalgodage2759--- via >> ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> > >> > Dear ChimeraX Dev Team, >> > >> > I'm Himal Godage, and I am currently in the process of >> developing a bundle for ChimeraX software. I have been thoroughly >> following the provided documentation, successfully completing the >> steps related to setting up a ChimeraX development environment, >> obtaining the code, and compiling ChimeraX. However, I have >> encountered a challenge in the IDEs, Debugging, and Profiling >> section, specifically within PyCharm. Following the provided >> steps, I am instructed to: >> > 1. Create a new Run/Debug Configuration. >> > 2. Set the script path field to point at a module. >> > 3. Set the module to “chimerax.core”. >> > 4. Set the Python interpreter to ChimeraX’s internal Python. >> > 5. Uncheck “Add content roots to PYTHONPATH”. >> > 6. Uncheck “Add source roots to PYTHONPATH”. >> > While attempting to follow these instructions, I encountered >> difficulty in locating the "chimerax.core" module. Unfortunately, >> the provided directory structure or module seems to be difficult >> to find in my current project. However there is a module named >> core in the following path. ChimeraX > src > bundles > core >> > >> > I am reaching out to seek your guidance on resolving this >> issue. Could you please provide insights on how I can locate or >> create the necessary "chimerax.core" module or suggest an >> alternative approach to address this problem? >> > >> > Thank you in advance for your time and support. >> > Best regards, >> > >> > Himal Godage >> > himalgodage2759(a)gmail.com >> > _______________________________________________ >> > ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >> > To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >> > Archives: >> https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >> > >> >

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Commands not working
by Heinen, Cobey J 28 Feb '24

28 Feb '24

Hello, I am new to this program and am learning the commands. However, when I type the commands from the tutorial, they don't work. For instance, when I do "start<https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/start.html> Side View" it registers it as an unknown command. Also, when I do the command "color hot pink :lys", it says it does not know what the residue is. Am I missing anything? Thank you for your time. Best, Cobey Heinen

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