- ChimeraX-users - RBVI Mailing Lists

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 23 Jun '24

23 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 11 Jun '24

11 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.

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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.

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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

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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

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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.

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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

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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

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