- ChimeraX-users - RBVI Mailing Lists

How probe radius should affect exposed surface area?
by Alon BenDavid 25 Dec '24

25 Dec '24

Hi, I am trying to measure the exposed surface area of lysine residues in DNaseI (4AWN). I am using the "measure sasa" command. To my surprise, when I am increasing the probe radius (1.4 A, 5 A, 10 A etc.) I receive larger exposed surface area. Is that OK? Many thanks, Alon

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cartoon style setting
by junjie han 23 Dec '24

23 Dec '24

Hi, May I ask how I can set the cartoon thick for a specific region of a structure in ChimeraX? For instance, the command "cartoon style #1/A:10-20 thick" plays an effect on the whole #1 molecule, not only affecting the specific region #1/A:10-20. Please let me know what the appropriate command is by any chance. Thanks, Junjie

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"straightening" or stretching disordered residues from alphafold models
by Daniel Elnatan 19 Dec '24

19 Dec '24

Hi folks, I’ve been playing around with AlphaFold to get protein structures and visualizing them in ChimeraX. For some proteins with a lots of disordered regions (e.g. between non-interacting, well-folded domains), the ‘noodles’ end up being a visual clutter. So I wrote a custom python function to be used in ChimeraX that would ‘straighten’ or stretch selected residues (typically the disordered or low pLDDT regions) by simply assigning torsion angles for a more ‘straight’ structure. I do this via the `Residue.set_phi()` and `Residue.set_psi()` methods. Here’s a link to my Python script: https://github.com/delnatan/colabfold_chunker_utils/blob/65f2419425de300df5… The command is run simply with `straighten #1:13-20`. Now when there are multiple chains within the same model, altering the torsion angles may actually move the relative positioning between the chains. Is there an easy way to avoid this? perhaps by passing an extra argument as ‘reference’ so one can place the structure back to its original coordinate for the reference residues. I’m not too familiar with the programming API just yet, but what is the correct way to do this? Maybe that the reference coordinates can be saved before assigning the torsion angles, and a transformation matrix can be computed only for the reference region between the original and moved structure. The altered chain can then be moved back by applying this transformation matrix? Thanks! -Daniel

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Help with ChimeraX modeling
by Christman, Nick 18 Dec '24

18 Dec '24

Hello, I am a graduate student at Indiana University, and I am trying to use ChimeraX to visualize positively charged surface accessible residues on some protein models. I've been trying to find the right combination of commands to get this to work but haven't been successful. I know how to calculate surface accessible residues, how to color the surface accessibility of residues within a selection on my model, and even how to calculate hydrophobicity of residues (related to charge), but I cannot figure out how to model the charge of surface exposed residues. Could you please point me in the right direction so I can get the models that I would like? Thanks! Nick Christman (He/Him) Dalia Lab Indiana University

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poc file of castp not support
by Prem Dorjee Tamang 17 Dec '24

17 Dec '24

sir/madam this chimer_x version 1.8 and 1.9 both the tools not support the poc file just look in thes matter

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initial dark mode support
by Greg Couch 16 Dec '24

16 Dec '24

FYI, the ChimeraX daily build now has dark mode support. So if you set your desktop to use dark mode, ChimeraX should follow. It's a work in progress, and it depends on developer's making their code dark mode aware (eg., icons may need to be modified), but if you notice any black text on a dark background, please let me know. -- Greg

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Re: [chimerax-announce] ChimeraX version 1.9 has been released
by Elaine Meng 16 Dec '24

16 Dec '24

Hi Dietmar, Thanks for your comments. Unless you refer to data that must be kept private, it is best to send questions and suggestions to the chimerax-users mailing list (CC'd here) rather than to me or any other individual team member. That way the most relevent people can see/answer your question and other users can weigh in if they also wish for the same thing. You could use the Help menu to open the ChimeraX User Guide that is included with your download instead of googling the web. You can also use the context menu in each tool (or its Help button, if it has one), to open the ChimeraX manual page for that tool, and the "help" command to show the manual page for each ChimeraX command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/help.html> Unfortunately the ChimeraX Help menu does not have a search feature, although that is probably on our list of requests already. Thanks, 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 Dec 13, 2024, at 12:29 PM, Dietmar Funck <dietmar.funck(a)uni-konstanz.de> wrote: > > Dear Elaine, dear ChimeraX developer Team, > > thanks for the release of ChimeraX 1.9. I am confident that it will be as great or even better than 1.8 :-) > > I have two requests/suggestions how your could improve ChimeraX further: > > a) the metal coordination function seems to be still missing in ChimeraX (or it is so well hidden that I wasn’t able to find it). > > b) You could teach Google that there is a difference between Chimera and ChimeraX. Each time, I try to find solutions to problems with ChimeraX, I get results from the user guide of Chimera, which usually don’t solve the problem. > > All the best, > > Dietma > > Dietmar Funck > Biopolymer Chemistry > Chemistry Department > University of Konstanz

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ChimeraX version 1.9 has been released
by Elaine Meng 13 Dec '24

13 Dec '24

UCSF ChimeraX version 1.9 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html Updates since version 1.8 (June 2024) include: - Foldseek search and analysis of large sets of similar structures - Find Cavities tool and "kvfinder" command to identify pockets and channels in macromolecules - optional residue-level summaries of H-bond and contact calculations - "mutationscores" command for analysis and plotting of results from deep mutational scanning - "surface hidefarblobs" command for colocalization analysis of light microscopy channels - raycasting option for medical images or other maps displayed as transparent volumes - selection can be expanded to all residues associated with the same column(s) in a sequence alignment - protein structure metadata can be updated with full chain sequences - missing-structure pseudobonds are labeled with the number of missing residues (default, can be turned off in preferences) For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog On behalf of the team, 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

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embed ChimeraX into web pages
by Marius Mihasan 12 Dec '24

12 Dec '24

Hi I have been using ChimeraX for some time to generate .stl files and print various molecules and molecular scenes. I planning/working on making the pdb to stl file conversion semi-automatic and more user friendly by offering the users some predefined 3D-printable renderings of the molecule of their choice as well as some simple push-buttons that would allow them to do some very simple customisation in the renderings. Everything needs to be packaged in a simple to acces web-page that can be used by educators and students . In a way similar to how NIHPresets work, but in a webpage. Or how NIH 3D QuickSubmit works, but more interactive. Is there a way to embed ChimeraX into web pages as it can be done with, for example, with JSmol (Jmol)? If yes, could someone please point me in the right direction? Thanks --------- Marius Mihasan, PhD. Habil. Professor, BioActive Research Group Biochemistry and Molecular Biology Laboratory, Faculty of Biology Alexandru Ioan Cuza University of Iasi Room B228, Carol I Blvd, no 20A, Iasi, Romania, 700506 Tel: +40(0)232202434 Fax: +40(0)232201472 http://cercetare.bio.uaic.ro/cadre/pagini-personale/marius.mihasan/index.ht… Associate Professor Darie Biochemistry & Proteomics Group Department of Chemistry & Biomolecular Science Clarkson University Potsdam, NY 13699-5810, USA mmihasan(a)clarkson.edu

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Chimerax install error
by 王康瑞 11 Dec '24

11 Dec '24

Greetings! I'm a student from Tsinghua university, thank you for your contribution. I encountered a error when I installing ChimeraX, and I pasted it in the attach files below. I was able to launch chimerax with option"--nogui", and "--help" option seems run successfully too, but the ui didnt work. Thank you! Best wishes, Kyrie.

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Question about translating/rotating individual chains in a model
by John Watters 11 Dec '24

11 Dec '24

Hi all, I was wondering if anyone had any suggestions on how to rotate and translate a DNA-bound protein model one base pair at a time (essentially walking the protein down the double helix) so I can compare its interactions with another protein. My plan was to define a vector between the center of mass of each nucleotide pair to then move the DNA-bound protein one average pitch length using the move command and rotation using the turn command one nucleotide at a time. When I try to save these new models using "save pdf_filepath.pdb models #3 relModel #1" the DNA-bound protein is still in the original position - do I need to modify the save command or move the DNA-bound protein using different commands? Thanks for any help you can provide! Best, John

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chimeraX 1.9rc202412100000 and copy/paste from the log panel not possible
by Vincent CHAPTAL 11 Dec '24

11 Dec '24

Hi, after upgrading to 1.9rc202412100000, I can't copy/paste a command from the log panel, typically the "view matrix" for the orientation. I tried it on 1.7 and it works with the 2 chimeraX sessions working at the same time. (haven't tried it on 1.8). Is there something specific I'm missing? I'm using macOS 14.6.1 Thank you Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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Z-flip option for fitmap?
by Oliver Clarke 11 Dec '24

11 Dec '24

Hi, I frequently use fitmap with global search to quickly fit an initial model to low resolution EM maps at early stages of data processing. At low resolution, it is often not immediately obvious which hand of the map is correct, so I will fit to both the original map and one that has been Z-flipped. Would it be possible to add an option to do this automatically, similar to how the "resolution" flag fits a molmap of the model at the specified resolution to the map? Cheers Oli

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display pseudobonds between atoms as solid line
by Vincent CHAPTAL 11 Dec '24

11 Dec '24

Hi, I've been playing a lot with the commands but I can't seem to get it right. I'd like to display a line between 2 atoms in a model. I tried: pbond #2.1:940@O #2.1:472@O reveal true color blue dashes 1 (and variations around it) but I got an error that pbond or pseudobond are unknown commands. I also played around with distance: distance #2.1:940@O #2.1:472@O hide #4.1 color #4 blue distance style #4 dashes 0 but the distance does not appear on my screen. Could you help me work this out? Thank you Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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Connecting ChimeraX to Cytoscape via your structureVizX.zip file
by Jean-François Bureau 11 Dec '24

11 Dec '24

Hi, I already use Chimera to cytoscape and I would like to add chimeraX. I downloaded your structureViZ.zip file and open it but I did not find what to do next. Thank you for your help Regards JF Bureau Institut Pasteur Paris, France

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Mac with nogui to run batch cmd
by aponysbc＠gmail.com 10 Dec '24

10 Dec '24

Hi, I'm trying to generate images in batch with chimerax from terminal on mac m2. When I run "chimerax --nogui --exit --cmd" I get the error: raise LimitationError("Unable to save images because OpenGL rendering is not available") chimerax.core.errors.LimitationError: Unable to save images because OpenGL rendering is not available ChimeraX command "graphics driver" gives: OpenGL version: 4.1 Metal -88.1 OpenGL renderer: Apple M2 OpenGL vendor: Apple Is there any way around this? I saw another post about this from 2020 that the nogui option only works on linux with offscreen. Is there any way to save images in batch from terminal? Thanks, Aaron

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Intra-chain contacts
by Rosaleen Calvert 10 Dec '24

10 Dec '24

Hi How do I get a text file of contacts A-B (NOT A-A or B-B). I have tried Show atoms Select Contacts Chain A on left. Chain B on right Uncheck intermodel Check file. Please help. Thanks. Rosy

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Error during flipping to change the handedness of the cryo-EM map
by Shardul Dhole 10 Dec '24

10 Dec '24

Hi, I was trying to change the map's handedness while trying to fit two maps in ChimeraX. However, when I use the command vop flip #3 (3 is my model number), it gives an error: *"**Expected a density maps specifier or a keyword." * How to overcome this? Thank You. -- Regards, Shardul Dhole.

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ChimeraX 1.8 release
by Elaine Meng 10 Dec '24

10 Dec '24

UCSF ChimeraX version 1.8 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/download.html Updates since version 1.7 (Dec 2023) include: - show worm depictions of attribute values (B-factor, conservation, etc.) using Render by Attribute tool or "cartoon byattribute" command - show attribute values with atomic radii using Render by Attribute or "size byattribute" - Select by Attribute graphical interface - Join Models generalized to any covalent bond (not just peptide) - show multiple alternate locations simultaneously with "altlocs show" - "pbond" command to create arbitrary pseudobonds - "measure contactarea" to report the area of one surface within a cutoff distance of another - Segmentations tool for interactive manual segmentation in 2D slice views, 3D (desktop), or 3D (VR) can be applied to any volume data, not just medical images; several fixes and ergonomic improvements including icons to assign/deassign mouse and VR hand-controller modes with a single click - set up and analyze batch AlphaFold predictions to search for protein-protein interactions (commands for advanced users who can run ColabFold directly on Linux) support for: - reading predicted aligned error (PAE) data from AlphaFold 3 - reading docking results from MOE - fetching atomic structures and maps from PDB-REDO - fetching/display of PDB NMR-STAR restraints For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog On behalf of the team, 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

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ChimeraX with Modeller
by Matt Goff 09 Dec '24

09 Dec '24

Hi Guys, I am trying to use ChimeraX with Modeller to fill in a few small gaps in my PDB file. However, when I run modeller from ChimeraX I get the following error: dyld[77819]: Library not loaded: /System/Library/Frameworks/Python.framework/Versions/2.7/Python Referenced from: <498CB722-A7BC-378D-A38D-3A690F9D635B> /Library/modeller-10.6/bin/mod10.6_mac10v4 Reason: tried: '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file), '/System/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file, not in dyld cache), '/Library/Frameworks/Python.framework/Versions/2.7/Python' (no such file) Exception in thread Thread-10 (threaded_run): 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/modeller/common.py", line 708, in threaded_run _ = subprocess.run(cmd, capture_output=True, text=True, check=True, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py", line 571, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/Library/modeller-10.6/bin/mod10.6_mac10v4', '/var/folders/wn/dw9ws1756cjfsv3p6m3lphmc0000gn/T/tmpj5w_luqj/ModellerModelling.py']' died with <Signals.SIGABRT: 6>. During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038, in _bootstrap_inner self.run() File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975, in run self._target(*self._args, **self._kwargs) File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/modeller/common.py", line 720, in threaded_run raise UserError("Modeller execution failed; output and errors in log") chimerax.core.errors.UserError: Modeller execution failed; output and errors in log It seems that the python2.7 is the issue, but I’m not sure which file to edit to point it to a new version (I’m on python 3.12). I’ve also tried this with ChimeraX 1.9 and 1.8 with the same error. Can you point me in the right direction? Thanks! Matt Goff

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Installing ChimeraX in a Apptainer container
by tluchko 08 Dec '24

08 Dec '24

Hello, I am trying to install ChimeraX in an apptainer (singularity) container. I am able to load molecules but running into two issues. - I get a lot of python tracebacks (see below). I have also installed ChimeraX directly on the same machine from the RPM and do not see these error messages. - Rendering is very slow, so I don't think it is using the graphics card. The direct installation is similarly slow, but I have installed VMD on the same system and I can tell that it is using the graphics card, both from the log and the speed. Please let me know if you have any suggestions to address either of these issues. This is the command that I am using to launch ChimeraX apptainer exec --bind /tmp/.X11-unix,/storage/storage1 --env DISPLAY=$DISPLAY --nv chimerax-rocky9.sif chimerax This is the definition file for the container. BootStrap: docker From: rockylinux/rockylinux:9.4 %labels Maintainer Tyler Luchko Version 1.0 %help This is a Rocky Linux 9 container for ChimeraX 1.8 %setup # These are only required if running on the HPC. #mkdir -p ${APPTAINER_ROOTFS}/tmp mkdir -p ${APPTAINER_ROOTFS}/scratch %post echo "Installing packages into the Rocky Linux 9 container" dnf -y install yum-utils dnf -y config-manager --set-enabled crb dnf -y install epel-release dnf -y install mesa-dri-drivers glx-utils dnf -y install /tmp/ucsf-chimerax-1.8-1.el9.x86_64.rpm dnf clean all %environment export PATH=/usr/bin:/usr/sbin:/bin:/sbin export SHELL=/bin/bash export LANG=en_US.UTF-8 Sample error output is below. Thank you, Tyler NOTE: available bundle cache has not been initialized yet NOTE: Traceback (most recent call last): File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 571, in start_tool ti = api._api_caller.start_tool(api, session, self, tool_info) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1286, in start_tool return cls._get_func(api, "start_tool")(session, ti.name) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/log/__init__.py", line 50, in start_tool return cmd.get_singleton(session, create=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/log/cmd.py", line 30, in get_singleton return tools.get_singleton(session, Log, 'Log', create=create) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/tools.py", line 216, in get_singleton tinst = tool_class(session, tool_name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/log/tool.py", line 161, in __init__ from chimerax.ui.widgets import ChimeraXHtmlView ImportError: cannot import name 'ChimeraXHtmlView' from 'chimerax.ui.widgets' (/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/ui/widgets/__init__.py) During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/tools.py", line 418, in start_tools bi.start_tool(session, tool_name) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 578, in start_tool raise ToolshedError( chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Log in bundle ChimeraX-Log: cannot import name 'ChimeraXHtmlView' from 'chimerax.ui.widgets' (/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/ui/widgets/__init__.py) BUG: Tool "Log" failed to start: chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Log in bundle ChimeraX-Log: cannot import name 'ChimeraXHtmlView' from 'chimerax.ui.widgets' (/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/ui/widgets/__init__.py) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/toolshed/info.py", line 578, in start_tool raise ToolshedError( _See log for complete Python traceback._ NOTE: UCSF ChimeraX version: 1.8 (2024-06-10) NOTE: © 2016-2024 Regents of the University of California. All rights reserved. NOTE: [How to cite UCSF ChimeraX](cxcmd:help help:credits.html) NOTE: Traceback (most recent call last): File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/triggerset.py", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/bug_reporter/crash_report.py", line 138, in _delayed_register_log_recorder _register_log_recorder(session) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/bug_reporter/crash_report.py", line 172, in _register_log_recorder log.record_to_file(log_file) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/log/tool.py", line 410, in record_to_file self._log_to_file(self.page_source) ^^^^^^^^^^^^^^^^ AttributeError: 'Log' object has no attribute 'page_source' BUG: Error processing trigger "new frame": AttributeError: 'Log' object has no attribute 'page_source' File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/log/tool.py", line 410, in record_to_file self._log_to_file(self.page_source) ^^^^^^^^^^^^^^^^ _See log for complete Python traceback._ Sent with [Proton Mail](https://proton.me/mail/home) secure email.

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Changing range for electrostatic potential coloring
by Eric Martz 07 Dec '24

07 Dec '24

I want to have less white and more color on an electrostatic potential map. I suspect this is done by reducing the range, but I can't find how to do this. I start with open 1bl8 fromDatabase pdb format mmcif select protein coulombic sel ui tool show "Surface Color" Then I have this dialog, where I have changed -10 ... +10 to -5 ... +5 When I click the Color button, I get "No map chosen for coloring", but the "using map" menu has no options. ??? Also I would like to re-color the surfaces for all 4 chains, not one at a time, but the "Color surface" menu seems to have 4 separate chain surfaces, but no option for all 4 at once. I will appreciate guidance! Thanks, -Erichttp://martz.molviz.org

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Coloring charged amino acids
by Eric Martz 06 Dec '24

06 Dec '24

Consider this: open 1pgb fromDatabase pdb format mmcifstyle sphereshow atoms 1. What is the command to hide all water? 2. How do I color charged amino acids, leaving uncharged one a neutral color (such as white)? I was hoping there was a menu item or command that would do something similar to this: color all whitecolor :lys,arg bluecolor :glu,asp redcolor :his lightblue without having to type all those commands. FirstGlance in Jmol and iCn3D have "one click" ways to do this, but I don't see one in ChimeraX or MolStar. Thanks, -Eric

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Deleting hydrogen
by Eric Martz 05 Dec '24

05 Dec '24

I have studied the help delete.html but have been unable to guess the command syntax to delete all hydrogen atoms. Unfortunately, that help page has no examples. Please tell me the command. Thanks, -Eric

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Centering?
by Eric Martz 05 Dec '24

05 Dec '24

I have spent over an hour failing to come up with the command that will move the molecule (and its center of rotation) to the center of the viewport. I see that "cofr all" places the center of rotation in the center of mass of what is loaded. But I have been unable to find the command to move it to the center of the viewport. I realize that I can drag it to approximate center of viewport with right-drag, but I'd like a command to do this. For example, load anything, drag it off center, then what is the command to move it back? Thanks, -Eric

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duplicate the map view
by Vitali James 04 Dec '24

04 Dec '24

Dear Chimera users I have to make a slice of a map on the selected atom. Is it possible to duplicate this map view? in chimeraX James

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Adding/editing chains' description
by André Graça 04 Dec '24

04 Dec '24

Hi everyone! I am missing a way to add/edit chain descriptions in ChimeraX. Is it possible? If not, would this be a reasonable request to plan for a future release? Wishing a nice day to whoever reads this message =) André ________________________________ From: chimerax-users-request(a)cgl.ucsf.edu <chimerax-users-request(a)cgl.ucsf.edu> Sent: Monday, December 2, 2024 10:52 PM To: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> Subject: ChimeraX-users Digest, Vol 96, Issue 1 Send ChimeraX-users mailing list submissions to chimerax-users(a)cgl.ucsf.edu To subscribe or unsubscribe via email, send a message with subject or body 'help' to chimerax-users-request(a)cgl.ucsf.edu You can reach the person managing the list at chimerax-users-owner(a)cgl.ucsf.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of ChimeraX-users digest..." Today's Topics: 1. Re: [Chimera-users] Movie from pdb file with 30 models of a conformational change. (Elaine Meng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 2 Dec 2024 13:52:23 -0800 From: Elaine Meng <meng(a)cgl.ucsf.edu> Subject: [chimerax-users] Re: [Chimera-users] Movie from pdb file with 30 models of a conformational change. To: Evan Kantrowitz <kantrow(a)bc.edu> Cc: Eric Pettersen via Chimera-users <chimera-users(a)cgl.ucsf.edu>, chimerax-users <chimerax-users(a)cgl.ucsf.edu> Message-ID: <0368B293-FF58-4F72-97C0-51DF75D23035(a)cgl.ucsf.edu> Content-Type: multipart/mixed; boundary="Apple-Mail=_5630A7C6-3B74-4E39-A0F1-3F2D7DF8DDB0" Hi Evan, Your image looks nice! From your screenshot I can see you are using ChimeraX (not Chimera) so I will answer for ChimeraX ( there is a different email address for ChimeraX questions, chimerax-users(a)cgl.ucsf.edu CC'd here). To "play" the conformational change there are a couple of options: (1) if the models are already open as a set of multiple models as shown in your screenshot, you can use command: mseries slider #1 ...which will open a slider interface that you can click play, record movie, etc. Or, you can play through the series with the "mseries" command. <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf…<https://rbvi.ucsf.edu/chimerax/docs/user/commands/mseries.html>> (2) Or, you can use the "coordsets true" option of the "open" command when opening the file, <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf…<https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#coordsets>> which means to interpret the file as a single trajectory instead of a series of models. That will automatically show a slider interface. Example: open blahblah.pdb coordset true If you want to use the file browser to find your PDB file, you can use command open browse coordsets true ...and it will open the file browser for you to find and choose the file. If you have a trajectory, you can also play through it with the separate "coordset" command. <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf…<https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html>> More info, general explanation of model series vs. trajectories <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Frbvi.ucsf…<https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.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 Dec 2, 2024, at 1:31 PM, Evan Kantrowitz via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > > Can someone give me help with a, I think, simple issue. I have a single pdb file containing 30 MODELS > These 30 models correspond to a conformational change. Here is a portion of the Models list-------------- next part -------------- A message part incompatible with plain text digests has been removed ... Name: PastedGraphic-1.png Type: image/png Size: 44782 bytes Desc: not available -------------- next part -------------- > > When I read it in,I see all 30 models showing in the view. > What I want to do is make a movie showing these 30 MODELS one after the other. I have tried coordset and coordset slider but have not got it to work. > > Thanks > > Evan > > PS. This is what the image looks like with the 30 frames.It was generated from the A chain of pdb files 2e2n and 2e2q using the website ViewMotions (viewmotions.bc.edu).-------------- next part -------------- A message part incompatible with plain text digests has been removed ... Name: PastedGraphic-2.png Type: image/png Size: 113501 bytes Desc: not available -------------- next part -------------- > > > ----------------------------------------------------------------------------- > Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu > Emeritus Professor of Chemistry Cell: 617-775-9915 > Boston College www2.bc.edu/evan-kantrowitz ----------------------------------------------------------------------------- ------------------------------ Subject: Digest Footer _______________________________________________ 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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.cgl.…<https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/> ------------------------------ End of ChimeraX-users Digest, Vol 96, Issue 1 *********************************************

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ChimeraX Download
by Wagner, Elina Lynge 04 Dec '24

04 Dec '24

Hello, I have been trying to download ChimeraX but get the error message that x64 is needed. I currently have a Microsoft Surface Laptop 7th Edition. The processor is Snapdragon(R) X 10-core and the system type is 64-bit operating system, ARM-based processor. Even though I have the 64-bit operating system, will I be unable to download the program due to having an ARM processor? If this is correct, will there be a version of ChimeraX that will be able to run on new windows 11 computers (surface pro 11 and surface laptop 7)? Have a great day, Elina Lynge Wagner The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender.

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Adding a label to MRC map file header
by Tom Goddard 03 Dec '24

03 Dec '24

Hi Raman, I'm not sure where in the MRC binary file this "EXPDATA EM" is suppose to go, maybe a "label" field. As you can see from the MRC file spec it has space for 10 labels in bytes 225-1024 of the header https://www.ccpem.ac.uk/mrc_format/mrc2014.php ChimeraX has no options to insert specified text into those labels, but you could edit the ChimeraX Python code that writes the MRC file to add a label. The file is called writemrc.py and is in your ChimeraX distribution, on Mac it is here ChimeraX.app/Contents/lib/python3.11/site-packages/chimerax/map_data/mrc/writemrc.py Here's what this code looks like in the ChimeraX Github repository https://github.com/RBVI/ChimeraX/blob/00c7ef34fdf8e3f9675cf892f346adbecbfe6… It has some lines that put a ChimeraX version and time stamp into the MRC file ver_stamp = 'ChimeraX %s %s' % (version, asctime()) labels = [ver_stamp[:80]] You could add a line after that labels.append('EXPDATA EM') to add a label with that string. then restart ChimeraX and save a map (e.g. command "save mymap.mrc"). Another approach would be to open the mrc file in a binary editor and carefully modify some of the bytes from 225-1024 to add your label. Of course all this assumes that EXPDATA EM is supposed to go in a label and not for instance the EXTRA bytes part of the header. It seems absurd that you have software that won't work without a special label in the file. Tom > On Dec 3, 2024, at 4:47 PM, Raman, C.S. <craman(a)rx.umaryland.edu> wrote: > > Hi Tom, > > Is there an easy way to insert into the header of an MRC file the descriptor "EXPDATA EM" as done by the PDB? I need to do this to run a validation program but don't quite know how to go about it. > > Any help would be greatly appreciated. > -raman

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Re: [Chimera-users] Movie from pdb file with 30 models of a conformational change.
by Elaine Meng 02 Dec '24

02 Dec '24

Hi Evan, Your image looks nice! From your screenshot I can see you are using ChimeraX (not Chimera) so I will answer for ChimeraX ( there is a different email address for ChimeraX questions, chimerax-users(a)cgl.ucsf.edu CC'd here). To "play" the conformational change there are a couple of options: (1) if the models are already open as a set of multiple models as shown in your screenshot, you can use command: mseries slider #1 ...which will open a slider interface that you can click play, record movie, etc. Or, you can play through the series with the "mseries" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/mseries.html> (2) Or, you can use the "coordsets true" option of the "open" command when opening the file, <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#coordsets> which means to interpret the file as a single trajectory instead of a series of models. That will automatically show a slider interface. Example: open blahblah.pdb coordset true If you want to use the file browser to find your PDB file, you can use command open browse coordsets true ...and it will open the file browser for you to find and choose the file. If you have a trajectory, you can also play through it with the separate "coordset" command. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> More info, general explanation of model series vs. trajectories <https://rbvi.ucsf.edu/chimerax/docs/user/trajectories.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 Dec 2, 2024, at 1:31 PM, Evan Kantrowitz via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > > Can someone give me help with a, I think, simple issue. I have a single pdb file containing 30 MODELS > These 30 models correspond to a conformational change. Here is a portion of the Models list > > When I read it in,I see all 30 models showing in the view. > What I want to do is make a movie showing these 30 MODELS one after the other. I have tried coordset and coordset slider but have not got it to work. > > Thanks > > Evan > > PS. This is what the image looks like with the 30 frames.It was generated from the A chain of pdb files 2e2n and 2e2q using the website ViewMotions (viewmotions.bc.edu) > > > ----------------------------------------------------------------------------- > Evan R. Kantrowitz, Ph.D evan.kantrowitz(a)bc.edu > Emeritus Professor of Chemistry Cell: 617-775-9915 > Boston College www2.bc.edu/evan-kantrowitz -----------------------------------------------------------------------------

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ChimeraX-1.8 functionality regarding the match command
by Nicholas Ferraro 02 Dec '24

02 Dec '24

Good morning, My name is Nicholas Ferraro. I am a graduate student at the City College of New York. I am currently using ChimeraX-1.8 to visualize multiple PDBs of the hexameric helicase I am working with. We have labeled each protomer of the hexamer A-F. I understand the software allows for matching structures either by best-aligning pair of chains, a specific reference structure to the best-aligning chain, and specific chains in a reference structure with specific chains in the matching chain. I have six PDBs. What I want to do is align all chains with respect to their chain ID and specific sequence. Can you advise on how to accomplish this in chimera-1.8? Thank you for you assistance. Please let me know if you need more details. Best, Nicholas Ferraro

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Stepping through model in secondary structure element steps (ISOLDE)
by Vorländer,Matthias Kopano 28 Nov '24

28 Nov '24

Dear all, I seem to remember that it was possible to step through a model in Isolde one secondary structure element at a time, however I don't find that option anymore. Is this possible at all? I prefer this to the isolde step option that goes through the model one residue at a time. Many thanks in advance, Matthias Sent from Outlook for Android<https://aka.ms/AAb9ysg> --- Matthias Kopano Vorländer Postdoc matthias.vorlaender(a)imp.ac.at<mailto:matthias.vorlaender@imp.ac.at> Plaschka Lab IMP - Research Institute of Molecular Pathology - imp.ac.at<https://imp.ac.at/> Part of Vienna BioCenter. www.viennabiocenter.org<https://www.viennabiocenter.org>

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Re: IMOD Segmentation to ChimeraX (.mod to .cmm Conversion)
by Tom Goddard 27 Nov '24

27 Nov '24

Glad you got it to work. Tom > On Nov 27, 2024, at 3:30 PM, LENKA MILOJEVIC <lenka11(a)g.ucla.edu> wrote: > > Dear Dr. Goddard, > > Thank you so much! That worked! I thought I’d have to produce a .cmm file or mask the map using the volume tool and the .mod file as a surface. > > I really appreciate your swift responses! This was incredibly helpful. > > Have a great rest of your day! > > Sincerely, > Lenka > > On Wed, 27 Nov 2024 at 15:26, Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: >> Hi Lenka, >> >> Seems like you got what you wanted "I was wondering if there's any way that I could convert the .mod file into a .cmm file because my goal is to segment a map in ChimeraX using the Color Zone tool, according to the contours from IMOD." Your image shows the traced curves as connected markers (fake atoms connected by bonds). To color the nearby density you would then use the Color Zone tool, menu Tools / Volume Data / Color Zone and it has a Split Map button that would let you make a new map that includes just the colored part near your curves. The equivalent ChimeraX command is "color zone" >> >> https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html#zone >> >> If the command syntax is confusing just use the graphical Color Zone tool and it will log the equivalent command to the Log panel and you will have a better idea of how to type a command if you want to use some of the fancier options (like bondPointSpacing) that the graphical tool does not offer. >> >> Tom >> >> >>> On Nov 27, 2024, at 2:46 PM, LENKA MILOJEVIC via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>> >>> In the event that I want to mask map #3 using the .mod file in #1 , which command exactly do I run? I'm attaching a screenshot showing my current session. >>> <image.png> >>> >>> >>> On Wed, Nov 27, 2024 at 2:42 PM LENKA MILOJEVIC <lenka11(a)g.ucla.edu <mailto:lenka11@g.ucla.edu>> wrote: >>>> Hi Elaine, >>>> >>>> If I don't input contours true, nothing shows up on my screen. It just states it read it. >>>> open <> C:/Users/lenkamilojevic/Box/HSV-1/Front/HSV1_9_overcoils.mod >>>> Read IMOD model C:/Users/lenkamilojevic/Box/HSV-1/Front/HSV1_9_overcoils.mod, pixel size 0.568 >>>> >>>> Sorry for the trouble. I really appreciate your help. >>>> >>>> Best, >>>> Lenka >>>> >>>> On Wed, Nov 27, 2024 at 2:09 PM Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >>>>> Hi Lenka, >>>>> Contours true is to make it into markers and links (fake atoms and bonds) instead of a surface. You do not need markers and links for masking, you only need a surface model (meshes true contours false). >>>>> >>>>> Just open the file directly without any options and by default it should make a surface model that you can use in "volume mask" - I thought "meshes true" would still make the surface but maybe it only does that when contours is false. >>>>> >>>>> I'm sorry I mentioned the contours option since it was confusing... I only did so because at first I thought you wanted markers. >>>>> >>>>> 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 Nov 27, 2024, at 1:34 PM, LENKA MILOJEVIC via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> > >>>>> > Dear Dr. Meng, >>>>> > >>>>> > Thank you! I've now managed to open the segmentation with open C:Path format imod meshes true contours true. But If I run volume mask it just outputs: >>>>> > volume mask #3 surfaces #1 fullMap true >>>>> > No surfaces specified >>>>> > volume mask #3 #1 extend 3 >>>>> > Missing required "surfaces" argument >>>>> > volume mask #3 surfaces #1 >>>>> > No surfaces specified >>>>> > >>>>> > Any advice? Is the contour not actually a surface yet? Or am I writing the command wrong. >>>>> > >>>>> > Thank you so so much! >>>>> > >>>>> > Best, >>>>> > Lenka >>>>> > >>>>> > On Wed, Nov 27, 2024 at 1:45 PM Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> wrote: >>>>> > Hi Lenka, >>>>> > The link that you sent is to the Chimera documentation (not ChimeraX): >>>>> > <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#object> >>>>> > >>>>> > Since they are different programs, there are differences... but not in this case! ChimeraX can also open these IMOD segmentations: >>>>> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#segmentation> >>>>> > <https://rbvi.ucsf.edu/chimerax/docs/user/formats/imod.html> >>>>> > >>>>> > These segmentation models are surfaces, not the atoms or pseudoatoms (markers) that you would need to define a zone with Color Zone. Although the second link above explains that you can make the IMOD surface mesh into markers/links by opening the file with the "open" command option "contours false," that is unlikely to make them suitable for defining zones. Mainly it is used to improve display. >>>>> > >>>>> > Instead you can use "volume mask" to mask parts of your map with the IMOD segmentation surfaces. >>>>> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#mask> >>>>> > >>>>> > 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 Nov 27, 2024, at 11:56 AM, LENKA MILOJEVIC via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >>>>> > > >>>>> > > Dear Sir or Madam, >>>>> > > >>>>> > > While the 'Input File Types' page lists .mod and .imod files under 3D objects ChimeraX can open, when I try to open a .mod file (e.g., run command open C:/*PathToFile* or through the GUI), the file doesn't show up even though the log output states 'Read IMOD model C:/*PathToFile*, pixel size X'. >>>>> > > >>>>> > > I was wondering if there's any way that I could convert the .mod file into a .cmm file because my goal is to segment a map in ChimeraX using the Color Zone tool, according to the contours from IMOD. >>>>> > > >>>>> > > I appreciate your time and assistance! >>>>> > > >>>>> > > Sincerely, >>>>> > > Lenka >>>>> > >>>>> > _______________________________________________ >>>>> > 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/ >>>>> >>> _______________________________________________ >>> 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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IMOD Segmentation to ChimeraX (.mod to .cmm Conversion)
by LENKA MILOJEVIC 27 Nov '24

27 Nov '24

Dear Sir or Madam, While the 'Input File Types' page <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/filetypes.html> lists .mod and .imod files under 3D objects ChimeraX can open, when I try to open a .mod file (e.g., run command open C:/*PathToFile* or through the GUI), the file doesn't show up even though the log output states 'Read IMOD model C:/*PathToFile*, pixel size X'. I was wondering if there's any way that I could convert the .mod file into a .cmm file because my goal is to segment a map in ChimeraX using the Color Zone tool, according to the contours from IMOD. I appreciate your time and assistance! Sincerely, Lenka Lenka Milojević Biophysics PhD Candidate Z. Hong Zhou Lab University of California, Los Angeles

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Closest distance list between residues/atoms; And selecting first/last residue in a chain
by pm676＠cam.ac.uk 27 Nov '24

27 Nov '24

Hi Is there a way by command line to generate a list of residue to residue (or atom to atom) distances ranked by closest to furthest, for say, all residues within 4A of each other at an interface between two protein chains? Can it also state the type of interaction, e.g. salt bridge, H-bond, vdW? Also, completely separately, is there a way by command line to select the first and last residue in a chain (without having to find their number)? No worries if not. Thanks so much! Cheers, Paul

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Visualization of methyls rotations
by Enrico Martinez 27 Nov '24

27 Nov '24

Dear ChimeraX users! In visualizing the MD trajectory, I noticed a small issue with the depiction of the rapid rotations of the ligand's methyl groups. Specifically, the hydrogens appear to periodically collapse into a singularity before returning to their expected positions. Could this be addressed through additional post-processing of the trajectory data? Many thanks in advance Enrico

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Question about using AF3-competitor outputs
by David S. Fay 26 Nov '24

26 Nov '24

Hi, Apologies if this already came up and I missed it. I just ran a few dimer models on the Chai Discovery website (https://lab.chaidiscovery.com/dashboard) and it seems to work quite well. However, when I tried to upload the relevant json file using the Structure Prediction - AlphaFold Error Plot pulldown menu, ChimeraX failed to recognize the file. I tried a few other files and something similar happened. Do you know of a workaround or is this something that is likely to get patched soon? I should mention that Chai may be putting the relevant PAE information into a “npy" file, (e.g., pae.model_idx_0.rank_1.npy) based on the size of that file, and I haven’t yet tried to convert npy to a json or know if that’s even possible. I also wonder if Boltz-1, another AF3 competitor, will have different outputs as well. They don’t seem to have a GUI yet and perhaps they won’t, so I haven’t been able tyo test this yet. I assume this has all been topic of discussions at ChimeraX though… Thanks in advance for your help! David David S. Fay Ph.D. Professor, Department of Molecular Biology Associate Director, National Institutes of Health Wyoming INBRE University of Wyoming email: davidfay(a)uwyo.edu

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How to remove specific H bonds
by Sen, Anindito 26 Nov '24

26 Nov '24

Dear ChimeraX group, How do I remove certain 'H' bonds from an atomic model, leaving the important 'H' bonds Regards Stay safe & Regards Anindito Sen. Ph.D

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Some questions about electrostatic potiential surface
by Quek 26 Nov '24

26 Nov '24

Dear Administrator, May I ask why the electrostatic potential surface I generated in Chimera X is entirely red without any blue? Is it because the electrostatic range is not set correctly? Could you tell me in which module I can set the range for the electrostatic potential? Additionally, how can I display the color scale for the electrostatic potential? Looking forward to your reply. Quek 1171543499(a)qq.com  

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RMSD between nonidentical atomic models
by Roden Deng Luo 26 Nov '24

26 Nov '24

Hi, If two atomic models do not have the exact same atoms, rmsd command does not run. One workaround would be to use matchmaker beforehand, and there is indeed a reported RMSD between "pruned atom pairs." However, this applies the matching before the calculation. In addition, from the attached screenshot (matching https://alphafold.ebi.ac.uk/files/AF-P32565-F1-model_v4.cif to 5wvi chain N), I expect most of the atoms should not be pruned, which is not the case. I wonder if there is a command or tool to calculate the RMSD between the not-moved nonidentical atomic models. Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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ChimeraX opening failure
by gianmarco.elisi＠gmail.com 25 Nov '24

25 Nov '24

Dear users, ChimeraX fails to open with multiple installation versions. The error with debug option that is shown is the following: Starting main interface Toolshed: find_bundle ChimeraX-Toolbar True None Toolshed: find_bundle ChimeraX-Toolbar True None Toolshed: find_bundle ChimeraX-Toolbar True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-Shortcuts True None Toolshed: find_bundle ChimeraX-SelInspector True None Toolshed: AvailableBundleCache.load: toolshed_url https://cxtoolshed.rbvi.ucsf.edu Toolshed: AvailableBundleCache.load: url https://cxtoolshed.rbvi.ucsf.edu/bundle/?uuid=e42ced0f-7162-57b1-9d35-4f49e… Toolshed: find_bundle ChimeraX-Core True None Windows fatal exception: access violation Thread 0x00004b9c (most recent call first): File "C:\Program Files\ChimeraX 1.8\bin\Lib\socket.py", line 836 in create_connection File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 945 in connect File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1451 in connect File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 979 in send File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1041 in _send_output File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1281 in endheaders File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1332 in _send_request File "C:\Program Files\ChimeraX 1.8\bin\Lib\http\client.py", line 1286 in request File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 1348 in do_open File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 1391 in https_open File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 496 in _call_chain File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 536 in _open File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 519 in open File "C:\Program Files\ChimeraX 1.8\bin\Lib\urllib\request.py", line 216 in urlopen File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\toolshed\available.py", line 62 in load File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\toolshed\__init__.py", line 467 in reload_available File "C:\Program Files\ChimeraX 1.8\bin\Lib\threading.py", line 975 in run File "C:\Program Files\ChimeraX 1.8\bin\Lib\threading.py", line 1038 in _bootstrap_inner File "C:\Program Files\ChimeraX 1.8\bin\Lib\threading.py", line 995 in _bootstrap Current thread 0x00005d04 (most recent call first): File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\ui\gui.py", line 315 in event_loop File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\__main__.py", line 1003 in init File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-packages\chimerax\core\__main__.py", line 1166 in <module> File "<frozen runpy>", line 88 in _run_code File "<frozen runpy>", line 198 in _run_module_as_main Any suggestion? Thanks

2 1

Overlay of specific chains
by Reza Khayat 25 Nov '24

25 Nov '24

Hi, We have multiple structures of a homo-hexamer (chains A-F). We'd like to overlay limited regions of each chain onto equivalent chains (e.g. residues 200-452 of chain A onto residues 200-452 of chain A). We're having difficulty identifying the correct syntax. Some of our structures align as desired while others are aligned according to the chain combinations that produce the lowest RMSD (e.g. residues 200-452 of chain A align onto residues 200-452 of chain C. Is it possible to restrict which chains align to which? Best wishes, Reza

2 1

VR on Apple silicon?
by David Bhella 22 Nov '24

22 Nov '24

Has anyone managed to make chimeraX VR work on an ARM Mac with meta quest 3? Possible or am I flogging a dead horse? D Professor of Structural Virology Associate Director - MRC-University of Glasgow Centre for Virus Research Director - Scottish Centre for Macromolecular Imaging Sir Michael Stoker Building Garscube Campus 464 Bearsden Road Glasgow G61 1QH Scotland (UK) Telephone: 0141-330-3685 Skype: d.bhella

2 2

protein void volume or enclosed space
by Vitali James 21 Nov '24

21 Nov '24

Dear Chimera support, Is it possible to calculate the enclosed space, channel volume or void space with the x-ray structure in chimera or chimera x. best, James

3 4

help browser and embedded pdf's
by John Monroe Heumann 21 Nov '24

21 Nov '24

Hi, Am I correct that ChimeraX help browser currently can not automatically open links to pdf's (requiring you to download the file instead)? If so, would this be a reasonable enhancement request or do the pdf reader licensing requirements make it impractical? Thanks! -jh-

3 5

ChimeraX on a tablet ?
by GOVAERTS Cédric 20 Nov '24

20 Nov '24

Hi ChimeraX team I wanted to know if ChimeraX can run on a tablet, either Ipad (M2 or M4 chips) of a Windows tablet (either Intel or Qualcomm Snapdragon) ? Obviously not for using it as main workstation, but rather check structural features while on the move. Thanks Cedric - Prof. Cedric Govaerts, Ph.D. Biochemistry & Structural Biology Universite Libre de Bruxelles - Campus Plaine. Building BC, Room 1C4 203 - Phone :+32 2 650 53 77 Boulevard du Triomphe, Acces 2 1050 Brussels - Belgium

3 6

Adding a Covalently Bound PLP to an AlphaFold Model
by Omar De Bei 20 Nov '24

20 Nov '24

Dear ChimeraX Community, I’m reaching out for advice on what is likely a simple issue, but I’m stuck and would greatly appreciate your input. I’m currently working on a PLP-dependent enzyme and have generated its structure using AlphaFold3. Unfortunately, AlphaFold3 does not include PLP as a preset ligand. To address this, I’m attempting to manually add the PLP to the predicted structure based on homology with other PLP-dependent enzymes. Here’s where I’m facing trouble: The PLP forms a covalent bond with a lysine residue in the active site. After aligning my AlphaFold-predicted structure with the PDB structure of a homologous enzyme, I managed to position the PLP within the predicted structure. However, the lysine residue is not in the correct orientation to form the covalent bond. I’ve tried changing the lysine’s rotamer to improve the position, but it’s still not quite right. I was considering performing a local minimization of the structure to refine the geometry, but I’m unsure how to do this in ChimeraX. Does ChimeraX offer a tool or feature for local minimization that could help in this scenario? If so, could you guide me on how to proceed? Thank you in advance for your help! Best regards, Omar

2 1

Bundle Sample Code
by Lou Holland 19 Nov '24

19 Nov '24

Hello, I work with Jon Agirre at the University of York and am about to start work on developing a privateer bundle for ChimeraX for glycan validation. I have been working through some of the very helpful tutorials and was planning to work through this page as I started building the bundle: https://www.rbvi.ucsf.edu/chimerax/docs/devel/writing_bundles.html I tried to download the sample code ( https://www.cgl.ucsf.edu/chimerax/cgi-bin/bundle_sample.zip) linked in the "Bundle Sample Code" section so that I could use it as a starting point to edit for the privateer bundle, but it seems that the sample code is not currently available. Is this something that you can help with? Best wishes, Lou Holland (Pronouns: they/them) Research Associate York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, YO10 5DD, York, UK

2 2

Question about commercial license for ChimeraX
by Gleb NOVIKOV 18 Nov '24

18 Nov '24

Dear ChimeraX Development Team, I hope this message finds you well. I am writing as an enthusiastic user of your remarkable software, which has been instrumental in both my academic and educational pursuits. Recently, I was approached by a small company interested in commissioning visualizations as part of a collaborative effort. I would like to inquire whether you offer a specific commercial license suitable for such freelance engagements. Additionally, I would be delighted to contribute to your website by sharing some of my visualizations of molecular systems, should this be of interest to your team. Thank you very much for your time and consideration. I look forward to your response. Best regards, Gleb

2 4

Question the lattest ChimeraX-1.9
by Enrico Martinez 18 Nov '24

18 Nov '24

Dear ChimeraX users! I am testing the new ChimeraX 1.9 release, via creating a short movie demonstrating an X-ray structure with basic features (without molecular dynamics). I noticed that my computer (using an Apple Silicon chip) gets quite hot during the frame rendering process (prior to encoding). In the previous release (1.8), the resource usage didn't seem as intense. Have there been any changes or optimizations in the new version that could explain this increased resource demand? Thank you in advance! Enrico

2 1

Fuzzy colour boundaries in protein cartoon
by James Lingford 18 Nov '24

18 Nov '24

Dear ChimeraX team and users, Is there a way to set colours of individual atoms to have a fuzzy boundary with the surrounding cartoon colour? Example picture attached. Normally, colouring individual atoms will create a solid line between one colour and the next. But is there a setting to change this? Many thanks

2 1

Modelling of missed loop fragments in multi-chain structure
by Enrico Martinez 18 Nov '24

18 Nov '24

Dear Chimera-X users! I need to predict missed loop fragments in a part of a multi-chain complex corresponded to GPCR bound to heteromeric G-protein (pdb id 8HTI). In this structure the chain A (a subunit of the G-protein) contain missed loop fragments. So the following commands were executed in command line to reconstruct the entire structure of this subunit: open 8hti seq chain /A ui tool show "Model Loops" modeller refine 1/A:1:internal-missing numModels 5 fast false adjacentFlexible 1 protocol standard which very slowly produces 5 models of the chain A. The problem was that the modeller considered the chain A in isolation from the rest of the structure and predicted loops overlapped with other chains of the G protein. Would it be possible to reconstruct the missing fragments in the chain A considering also the presence of other chains to build the full complex ? Many thanks in advance Enrico

3 15

adding a hydrogen to side chain of Glu
by Chang Jang 15 Nov '24

15 Nov '24

Hi ChimeraX users, I am building a customer peptide containing Glu, Ala, Lys using Build Structure. Once I built it, I added hydrogens. But, one oxygen in the side chains of Glu does not have a hydrogen added. How would I fix the structure? Thanks, Chang

2 2

2 different clipping planes, 1 per model?
by Vincent CHAPTAL 15 Nov '24

15 Nov '24

Hi, I wonder if it is possible to have 2 different clipping planes, 1 per model? It would be nice to show an helix as a surface within a domain like this. Thanks Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

2 1

the artifacts of the PBC of the MD trajectory
by Enrico Martinez 14 Nov '24

14 Nov '24

Dear Chimera-X users ! I am visualizing an MD trajectory of a biomembrane system obtained from Amber MD using the autoimage method of cpptraj. However, in this trajectory, I still observe very rapid lateral diffusion of certain lipids, which cross the entire system too quickly. Is there a way in ChimeraX to hide or suppress such motions for selected atomic groups (e.g., lipids)? Many thanks in advance Enrico

4 10

AlphaFold 3 source code released today
by Tom Goddard 11 Nov '24

11 Nov '24

AlphaFold 3 source code was released today AI protein-prediction tool AlphaFold3 is now open source <https://www.nature.com/articles/d41586-024-03708-4> https://github.com/google-deepmind/alphafold3 It is for non-commercial use only, and they require you to submit a form and get approved (2-3 days) to get the parameters. Tom

1 0

color bfactor by alphafold palette
by Agnieszka Obarska 11 Nov '24

11 Nov '24

Hi, I’ve just would like to let you know that we’ve noticed recently that alphafold palette in ChimeraX is not consistent with original AlphaFold coloring. Please see the slide attached. On the left there is a model colored by the “color bfactor pal alpha” command in ChimeraX while on the right there is the same model colored according to AlphaFold coloring scheme. Best, Agnieszka

5 16

New user -have queries
by karan kohli 11 Nov '24

11 Nov '24

Hi, Thank you for developing Chimera X, a tool that can help novices like myself to make in silico predictions. I am new to the world of silico protein interaction prediction. I am looking to use Chimera X to predict interaction between the antibody clones our company generated and the target protein. This should be doable with Chimera X right. I I am not sure how to do it. I am trying to follow the below video., But I am struggling to enter my ab sequence as it contains two chains (heavy and light). https://www.youtube.com/watch?v=TMcjEecFHaI I would really appreciate some help. Thank you, Karan

2 1

isolde write phenixRsrInput – how to restrain ligands?
by Shahid, Taha (Dr.) 08 Nov '24

08 Nov '24

Hi Tristan, I am trying to phenix real-space refine a structure containing AMPPNP, which I have modelled very accurately with ISOLDE. I create inputs using the isolde write phenixRsrInput command, including the restrainPositions true and includeHydrogens true arguments (which normally works perfectly). However, in this case, the Rsr output yields AMPPNPs with bond-length RMSZs > 2, although this is not the case in the input model itself. Would you be able to advise as to how I can potentially restrain the AMPPNP heavy atoms from the ISOLDE model as well? I am not a phenix expert, so not having to create these manually would be ideal. Perhaps a phenix command that will automatically generate an appropriate restraints file (to append to the isolde write phenixRsrInput command or phenix.real_space_refine itself), and/or lines that may be added to the real_space_refine.eff file created by ISOLDE? Any help would be immensely appreciated. Best regards, Taha

3 3

Re: [Chimera-users] Write out SeqRes entry
by Eric Pettersen 07 Nov '24

07 Nov '24

Hi David, For PDB output, ChimeraX should output SEQRES records for each chain as long as either: (A) the chain had sequence information in the original input file (e.g. SEQRES records), or (B) the chain has no missing-structure pseudobonds. I not the author of the mmCIF I/O part of ChimeraX, but I believe the criteria is different in that the chain has to have its "full_sequence_known" attribute set to true. You can do this "by hand" with the command (assuming your structure is model #1) "setattr #1 chains full_sequence_known true". --Eric Eric Pettersen UCSF Computer Graphics Lab P.S. There are different lists for Chimera vs. ChimeraX questions. I have cc'ed the ChimeraX list on this. > On Nov 6, 2024, at 10:54 AM, David Bhella via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Chimera/ChimeraX team, > > I have a model for an asymmetric unit of a virus capsid that has three chains of the same capsid protein – but I am having trouble depositing my model in the PDB because it only has a seqres entry for one of the three chains (B). Whatever I do, chimeraX will only write entries for that chain. Is there a way to force chimeraX (or any other program) to write the seqres card for each chain correctly? > > Thanks > D > > David Bhella > Professor of Structural Virology > Director, Scottish Centre for Macromolecular Imaging > Associate Director, MRC - University of Glasgow Centre for Virus Research > +44 (0)141 330 3685 <tel:+441413303685> > > > > > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu <mailto:chimera-users-leave@cgl.ucsf.edu> > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

3 2

Command to measure the Atomic to Map fit quality
by Roden Deng Luo 06 Nov '24

06 Nov '24

Hi ChimeraX Team, I wonder if there is a command that can measure the fit quality of an atomic structure to a volume map. I imagine the metric could be the sum of the density of all atoms or a correlation. Something like: fit_quality #ModelID in #VolumeID (similar to: rmsd #1 to #2). Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

4 6

Error saving a chimeraX session for large MD trajectory
by Enrico Martinez 06 Nov '24

06 Nov '24

Dear ChimeraX users! Dealing with the session contained loaded md trajectory of 10000 snapshots for a quite big system I got the following error trying to save this session File "/Applications/ ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.8.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-1.8.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-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 922, in save session.save(output, version=version, include_maps=include_maps) File "/Applications/ ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 651, in save fserialize(stream, data) File "/Applications/ ChimeraX-1.8.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 69, in cfunc.to_py.__Pyx_CFunc_8chimerax_4core_10_serialize_object__lParenobject__rParen_to_py_3obj.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 69, in cfunc.to_py.__Pyx_CFunc_8chimerax_4core_10_serialize_object__lParenobject__rParen_to_py_3obj.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.* Would it be possible to reduce the number of frames loaded as coordset e.g. closing the last 6000 frames ? Many thanks in advance! Enrico

2 4

Generating quantitative values for electrostatic potential and molecular lipophilicity potential
by mishra.ananya.163＠gmail.com 06 Nov '24

06 Nov '24

Dear Sir/Madam, I hope this message finds you well. My name is Ananya, and I am an undergraduate student working on a project analysing protein structures. I am currently exploring the tools available in ChimeraX to measure structural parameters of protein models. I find the visualization features for surface electrostatic potential and molecular lipophilicity potential especially valuable for my research, as they provide essential insights for my analyses. However, I have encountered some difficulty in locating a way to export quantitative values for these surface properties. Could you please advise if there is a method within ChimeraX to generate and export these values? Thank you for your time and I would greatly appreciate any guidance you could offer. Hope you have a great day ahead! Best regards, Ananya

3 8

integration of US-align into ChimeraX
by Chengxin Zhang 06 Nov '24

06 Nov '24

Dear ChimeraX developer. I am the developer of the US-align tool for protein and nucleic acid structure alignment. We currently offer a command line tool and a plugin for PyMOL. We are asked by the community to make a ChimeraX plugin. I have used ChimeraX for cryo-EM structure analysis before and know that there is a related tool called matchmaker. However, I do not know where to start to implement a matchmaker-like plugin for US-align in ChimeraX. Can you give me some recommendations and/or point me to a developer I can work with? Thanks. Chengxin Zhang, PhD Research Assistant Professor Department of Computational Medicine & Bioinformatics University of Michigan, Ann Arbor, MI

2 1

Variables and conditional statements in the command line
by Roden Deng Luo 05 Nov '24

05 Nov '24

Hello again, Are variables and conditional statements possible in the command line in any way? Thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

2 2

Troubleshooting the match function
by Christman, Nick 04 Nov '24

04 Nov '24

Hello, My name is Nick Christman and I am a microbiology PhD student at Indiana University. I am using ChimeraX to visualize and compare some small proteins (minor pilins) and it has been working great. I have run into an issue that I am hoping you can help me resolve. I want to use the match function to compare various different minor pilins. Each minor pilin has a somewhat unique structure, and I am trying to make the case that certain minor pilins from one organism are homologous to other minor pilins from a different organism. I have noticed that the match function provides different results from session to session. This concerns me and makes me question how much I can trust the results provided by chimeraX. Along with different spatial matching, the calculated RMSD values differ greatly. Is there a way I can make these matches more consistent? Like dictating a set starting point for matching? Thanks for your time! Nick Christman (He/Him) Dalia Lab Indiana University

2 1

setzoom command in Chimera X
by Vitali James 04 Nov '24

04 Nov '24

Dear Chimera support, There was a some old code to set the zoom in the chimera. I would like to set the same frame size of different models and different views in chimerax. How it can be done in chimeraX. best, James

2 1

Tool docking
by Eric Pettersen 01 Nov '24

01 Nov '24

Hi all, Starting with tomorrow’s daily build (but not the 1.9 release candidate or [eventual] production release), most tools can no longer be docked into the top or bottom areas of the main window, just the sides. This should prevent a lot of accidental grief from accidentally docking a tool into the toolbar area. This policy can be overridden by the tools themselves if typical use of that tool might involve docking into the top or bottom areas. Initially, two tools override the policy: the sequence viewer can be docked anywhere (since you might want it as wide as possible), and the tool created by the buttonpanel command can be docked into the top area, so that it can be placed next to the toolbar. If there are other tools that can really benefit from being docked into the top or bottom areas, please let me know. --Eric Eric Pettersen UCSF Computer Graphics Lab

2 2

Using name of selection with rmsd command
by Alexander Lee 01 Nov '24

01 Nov '24

Hello! I've been trying to use "sel sel res t; ~sel H; ~sel @N,CA,C,O; name target sel; sel #2:23; ~sel H; ~sel @N,CA,C,O; name original sel; rmsd target to original" to find the RMSD of just the target's side chain to the original, but I keep getting a reported RMSD of 0.000. I click on an atom of the target residue, then use "sel sel res t" to select the whole residue, "~sel H" to deselect hydrogens, " and "~sel @N,CA,C,O" to deselect the backbone. I then name the left-over selections. I thought this series of commands would work but it's giving me an incorrect RMSD. Is there a different combination I should try? Thank you, Alex

2 2

Coloring surface patches
by Radoslav Krivak 31 Oct '24

31 Oct '24

Hi I'm struggling with the following task. I want to display protein surface and color specific surface patches. More precisely, I want to: For each surface patch: 1. select specific solvent exposed atoms (by "Atom serial number" column from pdb file) 2. assign their surface a custom color (different color for each patch) A surface patch can contain atoms from 2 or more chains. Basically I'm trying to achieve something that looks like this: https://raw.githubusercontent.com/rdk/p2rank/refs/heads/develop/misc/img/p2… Is that even possible in ChimeraX? If it's not possible to select specific atoms by atom serial number I'd like to do it at least for residues. I’d be grateful for any help. Best regards Radoslav Krivak

2 1

Re: Smooth-MD script for a trajectory visualisation
by Enrico Martinez 29 Oct '24

29 Oct '24

Hello Eric, Just one extra question about the Smooth-MD script :-) Would it be possible to extend the idea of different smooth windows on different selections within the same model id (besides the version that we discussed applying for several different models).. For example, I have a complex system composed of membrane protein bound to a ligand embedded in explicit water and lipids. So, I divided all the components according to three different selections, which I would like smooth differently, in the following way: 1) protein & ligand (protein | :LIG) --> smooth with 5 windows 2) lipids according to amber naming (:PC,PE,PS, OL,PA) smooth with 6 windows 3) water and ions (:WAT|:NA*|:Cl*) smooth with 7 windows Would it be possible to do such tricky things using the same script? Many thanks in advance ! Enrico Il giorno sab 19 ott 2024 alle ore 02:55 Eric Pettersen <pett(a)cgl.ucsf.edu> ha scritto: > Hi Enrico, > Our servers have been down this week, so this is my first opportunity to > respond. So one possible approach is to change the "window = 10" line to: > > window_by_id = { (1,): 5, (2,): 10 } > > and change the 'if/continue' statement just inside the loop to: > > try: > window = window_by_id[s.id] > except KeyError: > continue > > The 'id' attribute of a model is a tuple of the model ID numbers, so for > model #1 it would be (1,), for model #2.2.1 it would be (2,2,1), etc. > So the try/except clause skips all models other than the ones you > explicitly put in the window_by_id dictionary. > > --Eric > > On Oct 11, 2024, at 1:32 PM, Enrico Martinez <jmsstarlight(a)gmail.com> > wrote: > > Hello Eric, > > I have an extra question about the Smooth MD script: I modified it abit to > apply the smoth effect only on a model with the name "ottimo.pdb" so that > it will affect only one selected model ( in the case when there are several > models in the same session ..) Here is this version enclosed. > > Could you suggest how it could be further modified to affect e.g. 2 models > via 2 different smooth windows e.g. smooth the model with the id 1 window=5 > and smooth the model with the id 2 with window2=10 ? > > Many thanks for help! > > Enrico > > Il giorno ven 8 dic 2023 alle ore 16:10 Enrico Martinez < > jmsstarlight(a)gmail.com> ha scritto: > >> Thank you very much Eric ! >> >> Cheers >> >> Enrico >> >> Le mer. 6 déc. 2023 à 19:02, Eric Pettersen <pett(a)cgl.ucsf.edu> a écrit : >> >>> Hi Enrico, >>> I have updated the smoothing script on the Scripts >>> <https://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts> page. If you get >>> a new version, there is a line near the top ("stride = 1") that you can >>> edit to make it use, say, every 5th frame ("stride = 5"). One issue is >>> that the coordinate set slider doesn't properly react to the change in the >>> number of frames. You have to close the slider and open a new one >>> ("coordset slider #1"). I will look into fixing that. >>> >>> --Eric >>> >>> On Dec 6, 2023, at 1:34 AM, Enrico Martinez via ChimeraX-users < >>> chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> and generally it would be visually fine with averaging of every N frame ? >>> well it would be interesting to test anyway :-) >>> >>> Cheers >>> >>> Enrico >>> >>> Il giorno mar 5 dic 2023 alle ore 19:30 Eric Pettersen >>> <pett(a)cgl.ucsf.edu> ha scritto: >>> >>> >>> Well, the smoothing script temporarily takes about triple the memory use >>> of the baseline trajectory, so I can imagine it crashing for a large >>> trajectory. Do you need 1000 frames? I could change the script to use >>> every Nth frame, which would use a lot less memory... >>> >>> --Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>> >>> On Dec 5, 2023, at 7:13 AM, Enrico Martinez via ChimeraX-users < >>> chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> update: I've just got a crash with md-smooth py script on chimera-x >>> working on a big system with > 1000 frames loaded in a single pdb >>> (with smaller trajectory there is no issues ..) >>> >>> Enrico >>> >>> Il giorno mer 15 nov 2023 alle ore 18:53 Eric Pettersen >>> <pett(a)cgl.ucsf.edu> ha scritto: >>> >>> >>> You are welcome. >>> >>> I don't think there is a "right" value for the window. A larger value >>> will provide more smoothing, while also creating more non-physical >>> geometries for highly mobile parts of the structure. A judgement call >>> really. >>> >>> --Eric >>> >>> On Nov 15, 2023, at 3:33 AM, Enrico Martinez via ChimeraX-users < >>> chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> Gotcha, thank you very much Eric ! >>> >>> BTW what is the value for the window that should be used ? Does it >>> mean that the higher value would result in smoother dynamics ? >>> >>> Enrico >>> >>> Il giorno mar 14 nov 2023 alle ore 19:47 Eric Pettersen >>> <pett(a)cgl.ucsf.edu> ha scritto: >>> >>> >>> Hi Enrico, >>> I don't see how you could get that error. I couldn't reproduce it >>> myself. I would need some kind of recipe for how you get it to occur. A >>> separate problem is that the averaging in the script isn't really right. >>> Line 21 of the script should be changed from: >>> >>> weight = window + 1 + abs(i-j) >>> >>> to: >>> >>> weight = window + 1 - abs(i-j) >>> >>> i.e. change the "+ abs(...)" to "- abs(...)". I have corrected the >>> script on the Scripts page. >>> >>> --Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>> >>> On Nov 14, 2023, at 6:31 AM, Enrico Martinez via ChimeraX-users < >>> chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> update: i've just opened closed chimera-x and reloaded my pdb and >>> everything works as expected. probably there is a bug somewhere .. >>> >>> Il giorno mar 14 nov 2023 alle ore 14:56 Enrico Martinez >>> <jmsstarlight(a)gmail.com> ha scritto: >>> >>> >>> Dear Chimera-X users. >>> >>> I am trying to record a md trajectory loaded as multi-pdb file: >>> >>> open ./stripped_traj2.pdb coordsets true >>> >>> I have the issue with smooth-md script (enclosed), which produces the >>> following error: >>> >>> open smooth_md_chX.py >>> open /home/test/Bureau/MOVIE_CHIMERAX\/smooth_md_chX.pyTraceback (most >>> recent call last): >>> File "/home/test/Bureau/MOVIE_CHIMERAX\/smooth_md_chX.py", line 23, in >>> <module> >>> avg += weight * coord_sets[j] >>> ValueError: operands could not be broadcast together with shapes >>> (6120,3) (6112,3) (6120,3) >>> >>> Should something be fixed in the script in order that I could observe >>> the MD movie with smooth details ? >>> >>> Thank you 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/ >>> >>> >>> >>> _______________________________________________ >>> 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 2

Sequence alignment and Extraction
by Mamadou Sangare 25 Oct '24

25 Oct '24

Dear, I would like to align two protein structures A and B, select and extract the parts of the B sequence that match A in a fasta file. Thank you for your support.

2 1

Visualisation of water near protein
by Enrico Martinez 25 Oct '24

25 Oct '24

Dear Chimera X users ! I have a question about the visualization of water around the protein. When I open the pdb + trajectory of the whale system, ChimeraX masks most of the water box, only showing some selected water molecules (probably involved in the interactions with the protein). Then, viewing the MD system, I can observe an exchange of this water, which is great ! Would it be possible via some command to modify the number of the displayed water in the beginning of simulation e.g. showing more water observed in the proximity to protein (..but still not the whole water box !) ? Many thanks in advance Enrico

2 4

Coloring by attribute
by Murugesh Narayanappa 24 Oct '24

24 Oct '24

Hi, I am Murugesh, a postdoctoral fellow in Dr. Rajat Rohatgi’s lab at Stanford University. I created an attribute file using z-scores and mapped these scores onto a structure, applying a gradient color scheme. However, I would like to know if there's a way to use discrete colors instead. Specifically, I want to apply a single color with uniform intensity for a selected range of z-scores (e.g., from 3 to 10) rather than using a gradient. I haven’t been able to figure this out. Is there an option or command I can try? I would appreciate any guidance. Thank you, Murugesh

2 2

Re: Inquiry About Translating ChimeraX GUI Language
by Zach Pearson 24 Oct '24

24 Oct '24

I think that was meant for Tom, I barely said anything, but thank you on his behalf and good luck with your translation project! We’re excited to see it. — Zach > On 24 Oct 2024, at 00:14, 刘俊骅 <273667986(a)qq.com> wrote: > > Dear Zach, > Thank you very much for your detailed and clear response. The direction you provided has been extremely helpful and will enable me to delve deeper into understanding these projects. I am excited to explore the code and see how I can customize the GUI interface to better suit my needs. > Your guidance has given me a great starting point, and I appreciate the time and effort you have invested in helping me. Your support is greatly appreciated, and it reinforces my enthusiasm for working with ChimeraX. > Once again, thank you for your assistance and for developing such an outstanding tool. Your work is truly making a significant impact on the scientific community. > Best regards, > Junhua Liu > > ------------------ 原始邮件 ------------------ > 发件人: "Zach Pearson" <zjp(a)cgl.ucsf.edu>; > 发送时间: 2024年10月23日(星期三) 凌晨2:35 > 收件人: "刘俊骅"<273667986(a)qq.com>; > 抄送: "ChimeraX Users Help"<chimerax-users(a)cgl.ucsf.edu>; > 主题: Re: [chimerax-users] Inquiry About Translating ChimeraX GUI Language > > A very cursory googling for ‘PyQt multilanguage’ brings up this repo: https://github.com/yjg30737/pyqt-multi-language-example but it is for PyQt5. > > Feel free to fork the ChimeraX repository and make pull requests. We would be eager to learn how to do this and turn it into a community-driven project. > > — Zach > > > On 22 Oct 2024, at 11:14, Tom Goddard via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > > > Hi Junhua, > > > > That would be great to add some Chinese language support in ChimeraX. We haven't looked into supporting languages other than English, but there are many Chinese speaking ChimeraX users. ChimeraX uses the Qt window toolkit which has "internationalization" support. Specifically ChimeraX uses the Python interface to Qt, called PyQt. If you figured out how to customize the ChimeraX GUI text we'd be interested in including that in ChimeraX. Your ChiimeraX distribution includes all the Python code which creates the user interface, so you could experiment with just changing the Python code in your distribution. The ChimeraX code is also on Github here > > > > https://github.com/RBVI/ChimeraX > > > > Here is the place in the code where the top level File, Edit, Select, Actions, Tools, ... menus are created. > > > > https://github.com/RBVI/ChimeraX/blob/1f1a0512d53424163992b53eadeffd2d9e39d… > > > > I guess the individual menu entries are added in many places in the code. For instance the File / Open... entry is here > > > > https://github.com/RBVI/ChimeraX/blob/1f1a0512d53424163992b53eadeffd2d9e39d… > > > > and it uses the add_menu_entry() function which probably is used to add all the menu entries > > > > https://github.com/RBVI/ChimeraX/blob/1f1a0512d53424163992b53eadeffd2d9e39d… > > > > Let us know what you figure out. > > > > Tom > > > > > >> On Oct 22, 2024, at 9:36 AM, 刘俊骅 via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > >> > >> Dear UCSF ChimeraX Developers, > >> I hope this email finds you well. > >> Firstly, I would like to express my sincere gratitude for developing such a powerful and versatile software as UCSF ChimeraX. It has been an invaluable tool for my research and visualization needs. > >> I have a question regarding the translation of the GUI interface language. I am interested in translating the interface into another language. Since I noticed that UCSF ChimeraX is based on Python, I was wondering if it is possible to modify certain .json, .py, or .xml files to change the displayed language. My intention is purely for personal use, and I have no plans to distribute or profit from any modifications. > >> Could you please provide any guidance or resources on how to achieve this? Any pointers or documentation would be greatly appreciated. > >> Thank you very much for your time and consideration. > >> Best regards! > >> Junhua Liu 273667986(a)qq.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/

1 0

Inquiry About Translating ChimeraX GUI Language
by 刘俊骅 24 Oct '24

24 Oct '24

Dear UCSF ChimeraX Developers, I hope this email finds you well. Firstly, I would like to express my sincere gratitude for developing such a powerful and versatile software as UCSF ChimeraX. It has been an invaluable tool for my research and visualization needs. I have a question regarding the translation of the GUI interface language. I am interested in translating the interface into another language. Since I noticed that UCSF ChimeraX is based on Python, I was wondering if it is possible to modify certain .json, .py, or .xml files to change the displayed language. My intention is purely for personal use, and I have no plans to distribute or profit from any modifications. Could you please provide any guidance or resources on how to achieve this? Any pointers or documentation would be greatly appreciated. Thank you very much for your time and consideration. Best regards! Junhua Liu 273667986(a)qq.com

5 6

Running_chimera_in_R
by Eric Pettersen 23 Oct '24

23 Oct '24

> From: Bipasa Show <bipasa.show22ug(a)apu.edu.in> > Subject: Running_chimera_in_R > Date: October 21, 2024 at 10:48:18 PM PDT > To: chimerax-users(a)cgl.ucsf.edu > > > Dear Team Chimera X, > Hope this email finds you well. I am reaching out in order to know if there is a way I can use R to automate specific processes in Chimera and Chimera X like structure-based sequence alignment, finding SASA for multiple residues etc. . It would be nice if you could let me know if automation in these softwares are possible using R. > Thanks and regards, > Bipasa

2 2

Problem with the coulombic protein
by svle＠tiscali.it 23 Oct '24

23 Oct '24

Hi, I have six representative frames, in pdb format , of six clusters evaluated with cpptraj of a trajectory . For three representative frames the command "coulombic protein" the surface is produced without any problem whereas for the remaining three I receive errors similar to the following text: coulombic protein Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue CYM (net charge -1) with am1-bcc method Running ANTECHAMBER command: /usr/lib/ucsf-chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /tmp/tmp76d1_frw/ante.in.mol2 -fi mol2 -o /tmp/tmp76d1_frw/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n (CYM) (CYM) Welcome to antechamber 20.0: molecular input file processor. (CYM) (CYM) Info: Finished reading file (/tmp/tmp76d1_frw/ante.in.mol2); atoms read (22), bonds read (21). (CYM) Info: Determining atomic numbers from atomic symbols which are case sensitive. (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac (CYM) (CYM) (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff (CYM) Info: Total number of electrons: 94; net charge: -1 (CYM) (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out (CYM) (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf-chimerax/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1 (CYM) (CYM) Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC (CYM) Charges for residue CYM determined Assigning partial charges to residue CYM (net charge -1) with am1-bcc method CYM: number of electrons (92) + formal charge (-1) is odd; cannot compute charges for radical species using AM1-BCC method Any suggestions to solve this problem? Thanks. Saverio

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Re: Mercator projection of MRC voluem coloured by attribute
by Tom Goddard 23 Oct '24

23 Oct '24

Hi Pranav, The image in my last email was created useing the 5 commands I listed in that email. The main drawback is it gives a 360 view from a point at the middle of the map looking out. So it can be used to see what the inside of a virus capsid looks like, but not the outside. My other suggestion about combining strips of a thousand images during a rotation is what would allow getting an outside 360 degree view. Tom > On Oct 23, 2024, at 10:40 AM, Pranav Shah <pranav.shah(a)strubi.ox.ac.uk> wrote: > > Love it! Thanks Tom, this might just work. WOuld you be happy to share the script you used to generate that stretched out view? > > > Best, > Pranav > -- > Pranav Shah > Post-doctoral Research Associate (PDRA) > Division of Structural Biology (STRUBI) > University of Oxford. > Center for Human Genetics, > Roosevelt Drive, > Oxford, OX3 7BN, UK > > ________________________________________ > From: Tom Goddard <goddard(a)sonic.net> > Sent: 22 October 2024 20:19 > To: Pranav Shah > Cc: ChimeraX-bugs(a)cgl.ucsf.edu > Subject: Re: [chimerax-users] Mercator projection of MRC voluem coloured by attribute > > Hi Pranav, > > I guess you mean you want to save a 360 degree projection image of your colored map? There is nothing quite like that in ChimeraX. If you want a 360 view from the center of the map you can get that with "camera 360" after positioning the view point in the middle of the map. For example > > open 1080 from emdb > color cylindrical #1 palette redblue > move z 350 > turn x 90 center #1 > camera 360 > > There is also command volume unroll that can unroll a cylindrical map. But it does not preserve coloring. And there was a flatten icosahedron capability that worked with atomic models in Chimera that is not in ChimeraX. > > https://www.cgl.ucsf.edu/chimera/experimental/flatten_icosahedron/flaticos.… > > For what you want you could spin the model around 360 degrees recording images each 0.2 degree, then have a script take the center column of pixels from each image and lay those columns side-by-side in a single image 1800 pixels wide. > > Tom > > Example of camera 360 giving view inside map EMDB 1080. > [emd1080.png][emd1080_360.png] > > On Oct 22, 2024, at 10:51 AM, Pranav Shah via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > hi Team, > This is potentially a left-of-center question, but is there a way I > could generate a mercator projection of an MRC volume that I have > colored by zone? I am happy to code this up in the chimerax python > environment, but I am not sure how I could access the voxel colour > information before projecting the volume. > > 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 > _______________________________________________ > 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

Installing plugins not working
by Oliver Clarke 23 Oct '24

23 Oct '24

Hi, Since the website came back, I can't get installing external tools (e.g. Clipper, ISOLDE) to work - is it just me or down for others also? It says it is downloading the bundle when I click install, but nothing happens after that. Cheers Oli

3 2

Mercator projection of MRC voluem coloured by attribute
by Pranav Shah 22 Oct '24

22 Oct '24

hi Team, This is potentially a left-of-center question, but is there a way I could generate a mercator projection of an MRC volume that I have colored by zone? I am happy to code this up in the chimerax python environment, but I am not sure how I could access the voxel colour information before projecting the volume. 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

2 1

placing a model at points defined in a CMM file
by Pranav Shah 22 Oct '24

22 Oct '24

hi Team, In addition to my previous question, is there a chimeraX function I could leverage to translate a pdb model to a point defined in a CMM file? 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

2 1

Viewing ccp4 volume data - Hiding outline box volume outside surface
by Stylianos Iliadis 22 Oct '24

22 Oct '24

Hello, I want to visualise a surface (isosurface) loaded from a ccp4 file on top of a protein binding site. When I load the volume and adjust the level properly, I can see the “correct” surface (visualised usually on Pymol), but this is only possible when I view slices of the volume=cube box. If I don’t use the sliced view, I only see a cube. Essentially, my question is how can someone hide the “negative” volume inside the cube box that is not part of the depicted isosurface? Thanks, Best, Stel Iliadis

2 1

Named selection problem
by Patrick Moynihan 22 Oct '24

22 Oct '24

Hi, I was hoping someone could help me with a persistent problem I am having. I am running ChimeraX version 1.8 (2024-06-10) on OSX. This problem has persisted for quite a while through several versions. If I work in ChimeraX and save a group of atoms as a named selection, it generally works as expected for the first group. After that, if I use the command “name XXXX” or define a selection via the GUI, it seems to take the input and reserve the name. However, when I return and select that named selection, the entire protein gets selected. I cannot for the life of me figure out why. I’ve tried low numbers of atoms and high, short names and long, the problem persists. Any advice would be appreciated. Thanks, Patrick

2 1

Set transparency of multiple models
by Ioannis Skalidis 22 Oct '24

22 Oct '24

Dear ChimeraX mailing list, I was wondering if there is a command to set the alpha (transparency) of multiple models (not maps). So far, I know that this is possible for maps through the transparency command, but the only way I know of to make a model transparent is to set each model alpha value individually in its color panel. Thanks for your help! Cheers, Dr. Ioannis Skalidis | Structural Biochemist | Twitter: @imjohnskal <https://twitter.com/imjohnskal> | johnskalidis(a)gmail.com

2 1

Query regarding Chimerax capablities
by Joseph Clifford 21 Oct '24

21 Oct '24

Hi Team, I hope this email reaches you well. I am a R&D scientist at Randox Laboratories and was wondering if possible could you model the nicked free form of PSA with the additional 7 amino acids at the N-term. I am exploring the capabilities of chimerax and want to put a business case together to my manager regarding this software application. [cid:54b7fcba-418a-438f-a6b0-5358e796c896] Many thanks in advance, Joseph Clifford This e-mail and any attachments are confidential and intended solely for the addressee and may also be privileged or exempt from disclosure under applicable law. If you are not the addressee, or have received this e-mail in error, please notify the sender immediately, delete it from your system and do not copy, disclose or otherwise act upon any part of this e-mail or its attachments. E-mail communications are not guaranteed to be secure or virus-free. Therefore Randox does not accept responsibility for any loss arising from unauthorised access to, or interference with, any e-mail communications by any third party, or from the transmission of any viruses. Randox does not accept liability for any errors or omissions in the contents of this message which arise as a result of e-mail transmission. Replies to this e-mail may be monitored by Randox for business and operational purposes. Any opinion or other information in this e-mail or its attachments that does not relate to the business of Randox is personal to the sender and is not given or endorsed by Randox.

2 1

Inquiry on Setting Clipping Caps for Helix in Cylinder Visualization
by youngxiaolin 18 Oct '24

18 Oct '24

Dear Sir/Madam, I am currently working on a cross-sectional visualization of a transmembrane helix bundle shown as cylindrical cartoon. I notice that, unlike in surface visualizations, my helices are not capped, leaving the ends exposed. Are there specific parameters or settings within ChimeraX that I should adjust to customize the appearance of the helix caps? Thank you in advance for your assistance. I am looking forward to your expert advice. Best regards, Xiaolin Yang National clinical research center for Infectious diseases

2 1

Issues accessing your websites
by Karp Mike (External) 18 Oct '24

18 Oct '24

Hi, We've been trying to install a chimerax plugin over the last few weeks and noticed we were unable to access the webpage the application tries to open (ChimeraX Toolshed). We checked and found this wasn't accessible from multiple internet connections. I've since noticed we are also unable to access any content on https://cgl.ucsf.edu Are you aware of an issue with your web sites? Regards, Mike. ________________________________ Legal Notice: This electronic mail and its attachments are intended solely for the person(s) to whom they are addressed and contain information which is confidential or otherwise protected from disclosure, except for the purpose for which they are intended. Dissemination, distribution, or reproduction by anyone other than the intended recipients is prohibited and may be illegal. If you are not an intended recipient, please immediately inform the sender and return the electronic mail and its attachments and destroy any copies which may be in your possession. UCB screens electronic mails for viruses but does not warrant that this electronic mail is free of any viruses. UCB accepts no liability for any damage caused by any virus transmitted by this electronic mail. (Ref: #*UG1107) [Ref-UG1107] ________________________________

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Fwd: 3d glasses free monitors from acer....
by Tom Goddard 18 Oct '24

18 Oct '24

Hi Krish, Ok. I fixed the first error which was caused by the Acer display OpenXR saying it did not have valid position and orientation data for the viewer. ChimeraX did not handle that correctly since VR headsets never have that problem. It might mean that eye tracking of the Acer display did not see your eyes so it did not know your viewing position. Or it could mean the Acer display never provides both position and orientation. If it never provides position and orientation of the viewer then the fixed code still won't render anything and we'll have to do more work to figure out how you are are supposed to get the view direction. The fixed XR code will be in daily builds dated October 17, 2024 or newer. Tom > > >> On Oct 16, 2024, at 2:53 PM, Krishnan Raman <RKrishnan(a)BIOCRYST.com> wrote: >> >> Hi Tom, >> I am willing it work with it till it gets resolved. It might open the display for other applications as well. >> Thanks again for your prompt responses. >> krish >> >> From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> Sent: Wednesday, October 16, 2024 4:14 PM >> To: Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> >> Subject: Re: [chimerax-users] 3d glasses free monitors from acer.... >> >> [EXTERNAL] >> >> Hi Krish, >> >> That is some progress. I see why ChimeraX gives that error. It is looking for if the OpenXR connected device does both position and orientation tracking (for VR headsets) and your display says it doesn't do at least one of those and then the ChimeraX code breaks. I may be able to fix that and see if you get further. I say "may" because the ChimeraX code is designed for VR where the headset has a position and orientation in space that is reported. If the Acer display doesn't give a position and orientation for the person's head using its eye tracking then the ChimeraX code would need to do something different to decide the view point. If I had a display I could explore it, but without one it will be hard to figure out. If you want to replace some ChimeraX Python code I can give you some that will help figure out the issues, but it may take a lot of back and forth of you trying code to get anywhere. >> >> Tom >> >> >> >> On Oct 16, 2024, at 1:40 PM, Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> wrote: >> >> SpatialLabs User Guide (acer.com) <https://link.edgepilot.com/s/e6a7c1ed/uvnt1Jd_IECk7VUP7-Ti6Q?u=https://spat…> >> >> <image001.png> >> >> Also, >> Tried XR on. The display froze but did go into the 3D mode. Chimerax is recognizing the driver and the monitor. I got an error while reporting this bug. So pasting it here. >> >> >> An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command "graphics restart" after changing the settings that caused the error. >> >> 'XR' object has no attribute '_eye_view_states' >> >> Traceback (most recent call last): >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\core\updateloop.py", line 84, in draw_new_frame >> view.draw(check_for_changes = False) >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\graphics\view.py", line 188, in draw >> self._draw_scene(camera, drawings) >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\graphics\view.py", line 231, in _draw_scene >> camera.set_render_target(vnum, r) >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\vive\xr.py", line 941, in set_render_target >> self._start_rendering() >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\vive\xr.py", line 796, in _start_rendering >> if not xr.start_frame(): >> ^^^^^^^^^^^^^^^^ >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\vive\openxr.py", line 372, in start_frame >> self._end_xr_frame() >> File "C:\Program Files\ChimeraX 1.8rc202406072045\bin\Lib\site-packages\chimerax\vive\openxr.py", line 446, in _end_xr_frame >> eye_view = self._eye_view_states[eye_index] >> ^^^^^^^^^^^^^^^^^^^^^ >> AttributeError: 'XR' object has no attribute '_eye_view_states' >> >> From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> Sent: Wednesday, October 16, 2024 12:10 PM >> To: Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> >> Cc: Greg Couch <gregc(a)cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>>; ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> >> Subject: Re: [chimerax-users] 3d glasses free monitors from acer.... >> >> [EXTERNAL] >> >> Hi Krish, >> >> I would hope the Acer SpatialLabs 3D display could render with the standard sequential stereo used with old LCD shutter glasses or polarized glasses systems. ChimeraX can output that using command "camera stereo". But I didn't seen any indication in searching online that they support that. Nor did I see any mention of them supporting the standard side-by-side stereo format which ChimeraX can also output (camera sbs). I would think the display would handle these format because 3D games use those. How could they not make it work with 3D games? What I did see online is that it works with OpenXR which is what virtual reality headsets use. That makes sense because the display offers eye tracking and the sequential or side-by-side stereo methods would not be able to use the eye tracking to change the viewing angle as you moved your head, while software that uses OpenXR will allow that. ChimeraX can uses OpenXR, command "xr on". I did not see online what software you use with the display to work with OpenXR. It would need some SpatialLabs OpenXR display control software running on your computer. Here is a bit of discussion about trying to use this display with another 3D app called Slicer >> >> https://link.edgepilot.com/s/cad1c1c9/DC6RKYZmHE2WohxUaEbXfw?u=https://disc… >> >> where the poster did get Slicer's OpenXR to show 3D with the display. >> >> Let me know what you figure out. If you find some technical reference for the display online that explains the types of 3D input it accepts or how to set it up to work with applications that use OpenXR, I'd be interested in seeing that documentation. If it works well my lab might get a display. >> >> Tom >> >> >> >> >> On Oct 16, 2024, at 7:35 AM, Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> wrote: >> >> Hi Tom, >> I got a new 3d glasses free monitor. >> Acer 27" SpatialLabs View Pro Stereoscopic 3D Monitor - Black - FF.R2CAA.002 - Computer Monitors - CDW.com <https://link.edgepilot.com/s/f5cca637/LqUzzf13mUCbZBJiJkeIJQ?u=https://www.…> >> I used the spatiallabs (GO app) software to see stereoscopic 3d images from Chimerax, coot(mapfitting) amd MOE. Seemd to work fine. >> The Go app converts any 2d to 3d stereo when the program displaying is set to fullscreen. >> The Spatiallabs software from acer has plugins for unity , blender and a few other software suites. >> The Go app is compatible with *.obj and Gitf 3d formats. I tried those from chimerax and the result is spectacular. >> Is there any possibility of getting a chimerax plugin? >> Regards >> Krish >> >> From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> >> Sent: Friday, July 12, 2024 1:22 PM >> To: Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> >> Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> >> Subject: Re: [chimerax-users] 3d glasses free monitors from acer.... >> >> [EXTERNAL] >> >> Hi Krishnan, >> >> We do not have any of the new 3D laptops to try ChimeraX. Let us know if it works. You will probably use the ChimeraX command "camera stereo" to put it into 3D model on one of these 3D laptops. >> >> Samsung also showed a 3D monitor at January's Consumer Electronics Show with rumors that it may come out this summer. Also don't know if ChimeraX will work on that display. >> >> While I think ChimeraX stereo is likely to work on these displays a problem with past stereo that used shutter glasses was that only workstation graphics cards could do stereo in a window, meaning that part of the display is showing 3D (e.g. the ChimeraX graphics pane) while the rest is showing 2D. This required special graphics driver support only offered in the workstation cards (like Nvidia Quadro) and not in the consumer cards. Full screen stereo where everything is rendered in 3D was available on consumer cards mostly for video games where everything is in 3D including user interface elements. >> >> Let us know if you get something working. >> >> Tom >> >> >> >> >> >> On Jul 12, 2024, at 8:56 AM, Krishnan Raman via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> https://link.edgepilot.com/s/22d26e4a/CHuCkVzwKkGj1oPV_qX5bQ?u=https://www.… >> >> maybe we can see chimerax😊 in 3d in these… they do have a plugin for unity.. Iam trying get one of these to try things out. >> >> 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. >> >> _______________________________________________ >> 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://link.edgepilot.com/s/bb15c3bf/yEg7mgqw30m5lBrfcz6VNQ?u=https://mail… >> >> >> >> Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning. >> >> >> >> 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. >> >> >> >> >> Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning. >> >> >> >> 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. >> >> >> >> >> Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning. >> >> >> >> 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. >> >

1 0

Question about creation of splines for alpha helix models
by Shriya Sivakumar 18 Oct '24

18 Oct '24

Dear Sir/Madam, My name is Shriya and I am an undergraduate research assistant at the Microsystems and Mechanobiology Lab at Carnegie Mellon University. I was wondering if you could help me with regard to how ChimeraX creates splines when modeling alpha helices. In particular, which atoms from the protein backbone are used as the points through which the spline is calculated? Thank you! Sincerely, Shriya Sivakumar

2 1

Re: 3d glasses free monitors from acer....
by Tom Goddard 18 Oct '24

18 Oct '24

Hi Krish, I would hope the Acer SpatialLabs 3D display could render with the standard sequential stereo used with old LCD shutter glasses or polarized glasses systems. ChimeraX can output that using command "camera stereo". But I didn't seen any indication in searching online that they support that. Nor did I see any mention of them supporting the standard side-by-side stereo format which ChimeraX can also output (camera sbs). I would think the display would handle these format because 3D games use those. How could they not make it work with 3D games? What I did see online is that it works with OpenXR which is what virtual reality headsets use. That makes sense because the display offers eye tracking and the sequential or side-by-side stereo methods would not be able to use the eye tracking to change the viewing angle as you moved your head, while software that uses OpenXR will allow that. ChimeraX can uses OpenXR, command "xr on". I did not see online what software you use with the display to work with OpenXR. It would need some SpatialLabs OpenXR display control software running on your computer. Here is a bit of discussion about trying to use this display with another 3D app called Slicer https://discourse.slicer.org/t/spatiallabs-stereoscopic-display/34800 where the poster did get Slicer's OpenXR to show 3D with the display. Let me know what you figure out. If you find some technical reference for the display online that explains the types of 3D input it accepts or how to set it up to work with applications that use OpenXR, I'd be interested in seeing that documentation. If it works well my lab might get a display. Tom > On Oct 16, 2024, at 7:35 AM, Krishnan Raman <RKrishnan(a)BIOCRYST.com> wrote: > > Hi Tom, > I got a new 3d glasses free monitor. > Acer 27" SpatialLabs View Pro Stereoscopic 3D Monitor - Black - FF.R2CAA.002 - Computer Monitors - CDW.com <https://www.cdw.com/product/acer-27-spatiallabs-view-pro-stereoscopic-3d-mo…> > I used the spatiallabs (GO app) software to see stereoscopic 3d images from Chimerax, coot(mapfitting) amd MOE. Seemd to work fine. > The Go app converts any 2d to 3d stereo when the program displaying is set to fullscreen. > The Spatiallabs software from acer has plugins for unity , blender and a few other software suites. > The Go app is compatible with *.obj and Gitf 3d formats. I tried those from chimerax and the result is spectacular. > Is there any possibility of getting a chimerax plugin? > Regards > Krish > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Friday, July 12, 2024 1:22 PM > To: Krishnan Raman <RKrishnan(a)BIOCRYST.com <mailto:RKrishnan@BIOCRYST.com>> > Cc: ChimeraX Users Help <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> > Subject: Re: [chimerax-users] 3d glasses free monitors from acer.... > > [EXTERNAL] > > Hi Krishnan, > > We do not have any of the new 3D laptops to try ChimeraX. Let us know if it works. You will probably use the ChimeraX command "camera stereo" to put it into 3D model on one of these 3D laptops. > > Samsung also showed a 3D monitor at January's Consumer Electronics Show with rumors that it may come out this summer. Also don't know if ChimeraX will work on that display. > > While I think ChimeraX stereo is likely to work on these displays a problem with past stereo that used shutter glasses was that only workstation graphics cards could do stereo in a window, meaning that part of the display is showing 3D (e.g. the ChimeraX graphics pane) while the rest is showing 2D. This required special graphics driver support only offered in the workstation cards (like Nvidia Quadro) and not in the consumer cards. Full screen stereo where everything is rendered in 3D was available on consumer cards mostly for video games where everything is in 3D including user interface elements. > > Let us know if you get something working. > > Tom > > > > On Jul 12, 2024, at 8:56 AM, Krishnan Raman via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: > > https://link.edgepilot.com/s/22d26e4a/CHuCkVzwKkGj1oPV_qX5bQ?u=https://www.… > > maybe we can see chimerax😊 in 3d in these… they do have a plugin for unity.. Iam trying get one of these to try things out. > > 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. > > _______________________________________________ > 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://link.edgepilot.com/s/bb15c3bf/yEg7mgqw30m5lBrfcz6VNQ?u=https://mail… > > > > Links contained in this email have been replaced. If you click on a link in the email above, the link will be analyzed for known threats. If a known threat is found, you will not be able to proceed to the destination. If suspicious content is detected, you will see a warning. > > > > 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 1

Chimerax Download
by Michael Gerber 18 Oct '24

18 Oct '24

To whom this may concern, Would it be possible to get the Chimerax zip download file for Windows? I have a school project I need to do it for and my presentation is coming up. Please and thank you! Best Michael

1 0

Odp.: problems with accessing server
by Leszek Wawiórka 18 Oct '24

18 Oct '24

I have just found information (https://x.com/ucsfchimerax) that the server is down for several days so the problem seems to be resolved 😉. Best regards Leszek ________________________________ Od: Leszek Wawiórka Wysłane: środa, 16 października 2024 08:20:32 Do: chimerax-users(a)cgl.ucsf.edu Temat: problems with accessing server Hallo there, I'm contacting You because I encounter permanent problem with my connection with your server. I would like to re-install both chimera and chimeraX packages but I can't get to your home webpage. There is error just saying ERR_CONNECTION_TIMED_OUT. I have checked the connection with ping www.cgl.ucsf.edu<http://www.cgl.ucsf.edu> saying that there is no delay. It seems that I can't connect with UCSF server through port 443. The port works for other servers. I have checked it for several different internet connections. Please advise me why its like that? and what is more important, is there any way to fix it somehow. I'd really appreciate your help. I look forward to hearing from you. All the best Leszek Wawiórka Department of Molecular Biologu University of Maria Curie-Sklodowska in Lublin, Poland dr Leszek Wawiórka<https://www.umcs.pl/pl/addres-book-employee,2923,pl.html> Uniwersytet Marii Curie-Skłodowskiej w Lublinie www.umcs.pl UMCS dba o środowisko. Jeśli nie musisz, nie drukuj tego dokumentu. Mejl może zawierać informację poufne, objęte prawem własności intelektualnej lub tajemnicą Uniwersytetu Marii Curie-Skłodowskiej w Lublinie. Jeśli nie jesteś jego adresatem, powiadom o tym nadawcę i usuń wiadomość. Wykorzystanie treści mejla lub załączników jest zakazane. Dziękujemy!

1 0

Question regarding licensing, when publishing data.
by Russ, Peter 14 Oct '24

14 Oct '24

Hi, I used your software for parts in an article where I also cited your requested quotes. The publisher wanted to confirm our licensing. In my understanding licensing is not a problem, as I am with the university for Stuttgart and don't earn money with this article. It would be nice if you could confirm this. Sincerely Peter Russ

2 1

Interface Residue Plot
by Reza Khayat 13 Oct '24

13 Oct '24

Hi, I'm hoping this question wasn't asked before. Is there a way to draw a dotted line between interacting residues? This would be similar to the Chain Interface graph that shows interaction between chains. Thanks. Best wishes, Reza Reza Khayat, PhD City College of New York Associate Professor Department of Chemistry and Biochemistry Co-Director NIH G-RISE program

2 1

saving a multi-model pdb with the subset of frames
by Enrico Martinez 11 Oct '24

11 Oct '24

Dear Chimera-X users! I am dealing with the visualization of a trajectory provided as the multi-model pdb contanained 3000 frames in multi-model format. How can I extract every 5th frame from a multi-model PDB file and save the reduced set of frames into a new PDB file, such that the new file contains five times fewer frames ? I've tried to do it like I did with the netcdf files but it does not work open ./my.pdb structureModel #1 step 5 Many thanks in advance Enriico

2 2

Support for _ma_qa_metric_local_pairwise to display PAE matrices stored in ModelArchive
by Gerardo Tauriello 11 Oct '24

11 Oct '24

Dear ChimeraX developers, Following up on discussions in https://github.com/chaidiscovery/chai-lab/issues/52 and the large amounts of models which have been deposited in ModelArchive (MA; https://modelarchive.org/) in the meantime, I would propose to support loading PAE (or other local-pairwise scores) values from ModelCIF files as used by MA. Here I link some examples which should capture most use cases: 1. ma-bak-cepc-0944<https://www.modelarchive.org/doi/10.5452/ma-bak-cepc-0944> includes 2 local-pairwise scores (PAE and "contact probability") and only stores scores for inter-chain residue-pairs. 2. ma-dm-hisrep-003<https://www.modelarchive.org/doi/10.5452/ma-dm-hisrep-003> includes a full PAE matrix. 3. In all cases in MA, entries contain a single accompanying zip file which also contains the local pairwise scores which are extracted into a separate file to keep the main ModelCIF file at a manageable size. The linked modelcif_examples_for_chimerax.zip<https://sibcloud-my.sharepoint.com/:u:/g/personal/gerardo_tauriello_sib_swi…> package includes pae_associated_file where the pairwise scores are directly in a separate file instead of being in a zip file and pae_in_main_file which includes the pairwise scores directly in the main ModelCIF file. Already now ChimeraX is able to parse the ma_qa_metric_local category in ModelCIF to do per-residue coloring for pLDDT etc which is awesome. To make sense of ma_qa_metric_local_pairwise one needs the following (I try to be detailed to simplify the implementation): 1. Parse ma_qa_metric and keep the IDs (_ma_qa_metric.id) for rows with ma_qa_metric.mode == "local-pairwise". If we want to restrict this to PAE matrices, one would additionally check that _ma_qa_metric.type == "PAE". 2. Look for the _ma_qa_metric_local_pairwise category. There are 3 options on where to find it: * Directly in the main ModelCIF file (as in pae_in_main_file/003-Spombe_H3-H4_tetramer_DPB3.cif). * In a separate file via _ma_entry_associated_files (as in pae_associated_file/003-Spombe_H3-H4_tetramer_DPB3.cif). You can find the file via _ma_entry_associated_files.file_url for the _ma_entry_associated_files row with file_content == "local pairwise QA scores". * In a separate file via _ma_associated_archive_file_details (as in all MA entries such as ma-bak-cepc-0944 and ma-dm-hisrep-003). Procedure to get it: * Find row in _ma_associated_archive_file_details with file_content == "local pairwise QA scores" and keep archive_file_id and file_path. * Find zip file in _ma_entry_associated_files with id == archive_file_id and download via file_url. * Fetch file named file_path from that zip file. 3. Within the _ma_qa_metric_local_pairwise extract scores for all given residue pairs for metric_id matching the desired IDs from step 1. Each residue is identified with model_id, label_asym_id, label_seq_id, and (redundantly) label_comp_id. There are no guarantees on the order of the data or completeness of the data but each referenced residue is guaranteed to exist in the atom_site category. Here is the current list of model sets in MA which include PAE matrices: ma-bak-cepc<https://modelarchive.org/doi/10.5452/ma-bak-cepc>, ma-coffe-slac<https://modelarchive.org/doi/10.5452/ma-coffe-slac>, ma-tbvar3d<https://modelarchive.org/doi/10.5452/ma-tbvar3d>, ma-ornl-sphdiv<https://modelarchive.org/doi/10.5452/ma-ornl-sphdiv>, ma-t3vr3<https://modelarchive.org/doi/10.5452/ma-t3vr3>, ma-low-csi<https://modelarchive.org/doi/10.5452/ma-low-csi>, ma-ombbaf2<https://modelarchive.org/doi/10.5452/ma-ombbaf2>, ma-rap-bacsu<https://modelarchive.org/doi/10.5452/ma-rap-bacsu>, ma-nmpfamsdb<https://modelarchive.org/doi/10.5452/ma-nmpfamsdb>, ma-jd-viral<https://modelarchive.org/doi/10.5452/ma-jd-viral>, ma-dm-prc<https://modelarchive.org/doi/10.5452/ma-dm-prc>, ma-dm-hisrep<https://modelarchive.org/doi/10.5452/ma-dm-hisrep>, ma-osf-ppp2r2a<https://modelarchive.org/doi/10.5452/ma-osf-ppp2r2a>. All together MA has over 200'000 models with PAE matrices which all supplement the AFDB in some way (e.g. protein complexes, viral proteins and other proteins not covered in UniProt). It would be great to include support for ModelArchive's ModelCIF files in ChimeraX and I am happy to provide further information and help as needed. Regards, Gerardo

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Re: [Chimera-users] Center and Orient
by Tom Goddard 10 Oct '24

10 Oct '24

You want sym #3 H,8,120,10,-5 as indicated in the documentation https://www.cgl.ucsf.edu/chimerax/docs/user/commands/sym.html Tom > On Oct 9, 2024, at 2:50 PM, Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> wrote: > > Also when tryng to give the symetry explicitly I get an error. Perhaps I am using the wrong syntax (??) > > sym #3 sym-type H,8,120,10,-5 > Expected a keyword > > Thanks > > > H. > > > ___________________________________ > Hernando Sosa, PhD. > Dept. of Biochemistry > Albert Einstein College of Medicine > 1300 Morris Park Av. > Bronx NY 10461 > phone (718) 430-3456 > emai: hernando.sosa@einsteinmed. <mailto:hernando.sosa@einsteinmed.org>edu > ___________________________________ > > > > From: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> > Sent: Wednesday, October 9, 2024 5:41 PM > To: Tom Goddard <goddard(a)sonic.net> > Subject: Re: [Chimera-users] Center and Orient > > I need to explicitly give the symmetry (helical) because the command > > > measure symmetry #1 set true (#1 is my map) > > reports: > > No symmetry found for my_map.mrc > > > H. > > > > From: Tom Goddard <goddard(a)sonic.net> > Sent: Wednesday, October 9, 2024 12:32 PM > To: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> > Cc: chimera-users(a)cgl.ucsf.edu List <chimera-users(a)cgl.ucsf.edu> > Subject: Re: [Chimera-users] Center and Orient > > CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. > Hi Hernando, > > Here is how to apply symmetry to one copy of an atomic model in a symmetric cryoEM map in ChimeraX. First use the "measure symmetry" command to determine the map symmetry, then use the "sym" command to make the symmetric copies of the atomic model. Here is an example > > open 8ofx > open 16862 from emdb > measure symmetry #2 set true > sym #1 symmetry #2 > > Tom > > > On Oct 9, 2024, at 7:52 AM, Hernando J Sosa via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Thanks Elaine, > > I will try to do this with ChimeraX. What I am trying to to do is to generate symetry related copies of a model fitted into a density map using the sym command. I noticed that the only way to define the center of symetry to be centered on the density volume was using the option center #n (where n is the id of the voume density) but only after doing center and orient by pressing the buttons in the volume viewer. > > Although chimeraX is much more prowerful I still find hard to find the the equivalent in ChimeraX of some operations that I use often in Chimera. 😉 > > Thanks again, > > Best > > H. > > _ > From: Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> > Sent: Tuesday, October 8, 2024 5:04 PM > To: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu <mailto:hernando.sosa@einsteinmed.edu>> > Cc: chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> > Subject: Re: [Chimera-users] Center and Orient > > CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. > > In Chimera, there may not be commands that do exactly the same thing as some button. You might look at "focus <model-number>" and "reset" (maybe only if one model is open, or they haven't been moved relative to one another?) but in my tests, they did not do exactly the same thing as those buttons. > > That's one reason ChimeraX is way better than Chimera! You can use the GUI and it shows the command that it used in the Log. > > Best, > 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 Oct 8, 2024, at 1:38 PM, Hernando J Sosa via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: > > > > Dear Chimera, > > > > What would be the equivalent commands to the Center and Orient buttons at the bottom of the Volume Viewer menu tab? > > > > Thanks > > > > H. > > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu <mailto:chimera-users-leave@cgl.ucsf.edu> > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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Oct 14-20 Chimera(X) website downtime
by Elaine Meng 10 Oct '24

10 Oct '24

Planned downtime for server maintenance: The Chimera and ChimeraX websites, Toolshed, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable starting Monday, October 14, 10 AM PDT and continuing for several days, potentially through the following weekend (October 14-20). Apologies for the inconvenience, 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

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Configuring ChimeraX AlphaFold “Fetch” and “Search” features
by Jim Thorpe 10 Oct '24

10 Oct '24

Hi ChimeraX Team In our commercial lab we are unable to access public domain AlphaFold databases, and instead have our own copy on-premises. Is there a mechanism to reconfigure the ChimeraX AlphaFold “Fetch” and “Search” features to query our in-house copy? ChimeraX error reported is: Fetching url https://alphafold.ebi.ac.uk/files/AF-Q5STB3-F1-model_v4.cif failed: HTTP Error 403: Forbidden Many Thanks for advising me Best Regards Jim [cid:image001.png@01DB1A36.151649E0] Jim Thorpe Scientific Investigator Protein, Cellular & Structural Sciences Target Discovery GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, SG1 2NY, UK james.h.thorpe(a)gsk.com [cid:image002.png@01DB1A36.151649E0]<https://www.gsk.com/> [cid:image003.png@01DB1A36.151649E0]<https://www.facebook.com/GSK> [cid:image004.png@01DB1A36.151649E0]<https://twitter.com/GSK> [cid:image005.png@01DB1A36.151649E0]<https://www.linkedin.com/company/glaxosmithkline> GSK monitors email communications sent to and from GSK in order to protect GSK, our employees, customers, suppliers and business partners, from cyber threats and loss of GSK Information. GSK monitoring is conducted with appropriate confidentiality controls and in accordance with local laws and after appropriate consultation.

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Changing dihedral angle
by Prathvi Singh 09 Oct '24

09 Oct '24

Hi Elaine, Is it possible to change the dihedral angle between any given four sets of atoms, say CA,CB,CG, HG2 of a Lysine residue using command line in either chimera/chmeraX? Thanks in advance, Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Re: [Chimera-users] Center and Orient
by Tom Goddard 09 Oct '24

09 Oct '24

The documentation explains how to measure symmetry for a helical map https://www.cgl.ucsf.edu/chimerax/docs/user/commands/measure.html#symmetry You have to use the helix option to give it some clue about the rise and twist angle per asymmetric unit step. Tom > On Oct 9, 2024, at 2:41 PM, Hernando J Sosa <hernando.sosa(a)einsteinmed.edu> wrote: > > I need to explicitly give the symmetry (helical) because the command > > > measure symmetry #1 set true (#1 is my map) > > reports: > > No symmetry found for my_map.mrc > > > H. > > > > From: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > Sent: Wednesday, October 9, 2024 12:32 PM > To: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu <mailto:hernando.sosa@einsteinmed.edu>> > Cc: chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> List <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> > Subject: Re: [Chimera-users] Center and Orient > > CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. > Hi Hernando, > > Here is how to apply symmetry to one copy of an atomic model in a symmetric cryoEM map in ChimeraX. First use the "measure symmetry" command to determine the map symmetry, then use the "sym" command to make the symmetric copies of the atomic model. Here is an example > > open 8ofx > open 16862 from emdb > measure symmetry #2 set true > sym #1 symmetry #2 > > Tom > > > On Oct 9, 2024, at 7:52 AM, Hernando J Sosa via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Thanks Elaine, > > I will try to do this with ChimeraX. What I am trying to to do is to generate symetry related copies of a model fitted into a density map using the sym command. I noticed that the only way to define the center of symetry to be centered on the density volume was using the option center #n (where n is the id of the voume density) but only after doing center and orient by pressing the buttons in the volume viewer. > > Although chimeraX is much more prowerful I still find hard to find the the equivalent in ChimeraX of some operations that I use often in Chimera. 😉 > > Thanks again, > > Best > > H. > > _ > From: Elaine Meng <meng(a)cgl.ucsf.edu <mailto:meng@cgl.ucsf.edu>> > Sent: Tuesday, October 8, 2024 5:04 PM > To: Hernando J Sosa <hernando.sosa(a)einsteinmed.edu <mailto:hernando.sosa@einsteinmed.edu>> > Cc: chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> > Subject: Re: [Chimera-users] Center and Orient > > CAUTION: This email comes from an external source; the attachments and/or links may compromise our secure environment. Do not open or click on suspicious emails. Please click on the “Phish Alert” button on the top right of the Outlook dashboard to report any suspicious emails. > > In Chimera, there may not be commands that do exactly the same thing as some button. You might look at "focus <model-number>" and "reset" (maybe only if one model is open, or they haven't been moved relative to one another?) but in my tests, they did not do exactly the same thing as those buttons. > > That's one reason ChimeraX is way better than Chimera! You can use the GUI and it shows the command that it used in the Log. > > Best, > 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 Oct 8, 2024, at 1:38 PM, Hernando J Sosa via Chimera-users <chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu>> wrote: > > > > Dear Chimera, > > > > What would be the equivalent commands to the Center and Orient buttons at the bottom of the Volume Viewer menu tab? > > > > Thanks > > > > H. > > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu <mailto:chimera-users-leave@cgl.ucsf.edu> > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

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How to remove a biological assembly from an atomic model
by Guillaume Gaullier 09 Oct '24

09 Oct '24

Hello, I am using the asymmetric unit of a PDB entry to define my own biological assembly based on a symmetric cryoEM map. Using the sym command, I can store the new biological assembly in the cif file. However, it seems I can't remove the biological assembly that came with the PDB entry's annotation, but that is now completely irrelevant because I moved the coordinates into my map (when I apply it, I get new chains completely outside the map). Is there a way to do this without needing to edit the cif file with a text editor? 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

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Images in background
by Enrico Martinez 08 Oct '24

08 Oct '24

Dear ChimeraX Development Team, I would like to extend my appreciation for your continuous work on ChimeraX and the powerful capabilities it offers for molecular visualization. I previously inquired about the possibility of using static images as backgrounds, similar to what is available in UCSF Chimera. Together, we discovered a workaround by loading an image as a model, adjusting its orientation, and setting it as a static background. However, there is still a significant limitation: when rotating a molecular model (defined in a separate model), the entire scene—including the background—rotates. This compromises the visual experience, as it disrupts the intended static nature of the background image. I would like to formally request the introduction of a more robust solution that allows for the following: - The ability to set static images as true background elements that remain fixed when manipulating other models (e.g., rotating or zooming in on molecular structures). - Support for short background animations, allowing users to load video or animated files that can play while the molecular models are rotated and manipulated independently. These features would greatly enhance the flexibility and presentation capabilities of ChimeraX, making it easier to create high-quality visualizations and presentations. I believe many users would benefit from these enhancements. Thank you for considering this request, and I look forward to any updates on the possibility of implementing these features. Yours sincerely Enrico

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Buried SAS Area selection
by Fernando Villa 07 Oct '24

07 Oct '24

Dear Chimera users I have been trying to select the atoms involved in the interface of a receptor/ligand complex in ChimeraX without success. In UCSF Chimera e.g. open 4RSC del solvent sel #0:.b del sel select ligand zr>10 del sel focus measure buriedArea protein ligand sel @/buriedSASArea “Only atoms at the interface are selected” = OK **The interface buried area calculation was performed and the atoms involved in the buried area were selected. However, I wish to do the same in ChimeraX, for surface area calculations: e.g. open 4RSC del solvent del /B select ::name="A3V" view sel measure buriedarea protein withAtoms2 ligand sel t list t cutoff 0 “All atoms in the interface are selected per residue” = KO The results of the calculations are the following: UCSF Chimera = 719.643 ChimeraX = 719.65 = OK I have difficulties to select only the atoms in the interface, not all atoms of the residues, I have tried several ways to do this but it has been complicated, I even tried to insert the command “sel @/buriedSASArea” of UCSF Chimera in ChimeraX without success. Sincerely. Fer <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Libre de virus.www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Color Zone
by Mark Rosenberg 07 Oct '24

07 Oct '24

Using an atomic model and map, when I colour a different zone, I "lose" the colour from the previous zone I coloured. Is this a bug? This is in Windows 11. Thanks in advance.

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3MF Support
by Conrad Toms 07 Oct '24

07 Oct '24

Hello, Is .3MF export support planned for ChimeraX? It is overall a superior format to STL and has been seeing adoption in most programs for mesh work and 3D printing.

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Software copyright issue
by 姜恩誉 06 Oct '24

06 Oct '24

Hello, I would like to ask whether chimera software academic free includes the publication of papers? Looking forward to your reply, thank you 姜恩誉 2023111025(a)stu.njau.edu.cn

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Web server down?
by Roden Deng Luo 05 Oct '24

05 Oct '24

Dear ChimeraX Team, I am making a tutorial and notice that I cannot access the download page again. This is probably the fourth time I experienced this in recent months. Best, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Functionality request: Measure molecular weight
by Jan-Hannes Schaefer 04 Oct '24

04 Oct '24

Dear ChimeraX community, Thanks for your work and effort in making ChimeraX available to all of us. I would love to see a function in future versions of ChimeraX to measure the molecular weight of the model and link it to the uniprot entry? Let me know if this is something you would like to add. Yours, Jan ___________________________ Jan-Hannes Schäfer, PhD Lander Group • Scripps Research 10630 John J Hopkins Dr. San Diego, CA 92121 Mailing-code: TRY-21 jschaefer(a)scripps.edu (858) 784-8728

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Selecting a sidechain but not the cartoon backbone
by James Lingford 03 Oct '24

03 Oct '24

Dear ChimeraX team, I want to select only the sidechains of a protein in order to visually outline them for a figure. This isn't an issue if cartoons are turned off, because I can select the only sidechains I want and use the command: `sel sel & sidechain` and I outline them in a nice way with... `graphics sel col black width 2` However, if cartoons are turned on then this won't select just the sidechain, but select a portion of the cartoon backbone too. I'm not sure how to specify this. Ideally I want a transparent cartoon with opaque sidechains, and then have only the sidechains selected. Please see the images attached for examples of what I'm referring to. Many thanks, James [image: sidechain2.png] [image: sidechain1.png] -- *James Lingford* | Research Officer, Greening Lab Department of Microbiology, Monash Biomedicine Discovery Institute Monash University Google Scholar <https://scholar.google.com/citations?user=4KSRHTUAAAAJ&hl=en> | Website <https://www.jameslingford.com/>

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Coloring chains by attribute
by Juan Ortiz Mateu 02 Oct '24

02 Oct '24

Dear developers, I’m trying to color the ribosome (4ug0) with a color code for abundance of each chain (ribosomal proteins) found in my proteomics data. I have created an attribute successfully, as it says in the log: Summary of feedback from opening fc.defattr note Assigned attribute 'FC' to 32 chains using match mode: any However, in the Render/Select by attribute tool there is no option to color chains, only atoms/residues/structures. How can I apply these numeric values to color the different chains/subunits? Thank you, ******************************** Juan Ortiz Mateu Researcher PhD Student Membrane Proteins Lab Biotecmed Institute University of Valencia Dr. Moliner, 50 46100 Burjassot (Valencia) Spain research.uv.es/membrana/ **********************************

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system log of ChimeraX
by Enrico Martinez 02 Oct '24

02 Oct '24

Dear ChimeraX users! I wonder if there is some system log file containing the full history of previously executed commands and scripts in Chimera-X on the linux machine ? This could be useful if I did not save something and would like to resolve the full story. All the best, Enrico

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Pre-fitted structures
by Eric Pettersen 01 Oct '24

01 Oct '24

Hi Randy, I'm attaching a wheel file where the Fit in Map tool (and phenix emplaceLocal command) supports pre-fitted structures. Use the "toolshed install <drag-and-drop wheel file>" command to install it. I guess I could now use an example system where emplace_local returns more than one solution, so I can work on a browsing interface for results. --Eric

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Chimera X opening issues on windows machineGood Afternoon,
by Haroon, Shohaib (NIH/NICHD) [C] 01 Oct '24

01 Oct '24

Good Afternoon, Hope this email finds you well. I am reaching out to your regarding an issue after successfully installed the latest version of Chimera X on one of my user he is using windows desktop and not able to open it. Even though I tried it multiple versions same issue persist. I installed the same version on my laptop without any issues and working fine. Is there anything need to do differently so it can open on desktop. Much appreciated for your help Thank you Shohaib Haroon Desktop Support Technician Information Resources Management Branch Eunice Kennedy Shriver National Institute of Child Health and Human Development 6710B Rockledge Drive, Bethesda, MD 20817 cell:301-275-0276 Email: shohaib.haroon(a)nih.gov<mailto:shohaib.haroon@nih.gov>

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Increasing ChimeraX speed?
by Altobelli, Chad 30 Sep '24

30 Sep '24

Hi, I love using ChimeraX to make morphs, but my protein is quite a large hexamer (500kda) and the progression through the coordset can be quite slow during playback. When I look at my Windows taskmanager, I can see that neither my CPU (12th Gen Intel i7-12700H), RAM, or GPU (NVIDIA RTX 3050 Laptop) are maxed out. Is there a way to speed up Chimera morphs? Thanks, Chad

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Molecular Dynamics in ChimeraX
by Enrico Martinez 30 Sep '24

30 Sep '24

Dear ChimeraX users! I noticed that in ChimeraX there is no built-in molecular dynamics simulation engine as opposed to the older UCSF Chimera. Is it possible to use some visualization trick to deform slightly static coordinates of atomic selection introducing (visually) the impression that they move during movie recording ? Many thanks in advance Enrico

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Software copyright consulting
by 姜恩誉 27 Sep '24

27 Sep '24

Hello, is the application of your Chimera X software for paper publication a non-commercial use？ Looking forward to your reply. Thank you 姜恩誉 2023111025(a)stu.njau.edu.cn

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info distmat command
by NUR AIDA SAKINAH 27 Sep '24

27 Sep '24

Hi ChimeraX teams, Can you guide me to use the *atoms-spec* for info distmat command. I want the output in chimerax log to list out distances between drug compound and the amino acids side chains and only display the distances below than 4 A. For now, what i have got, the output include distances between atoms in the drug itself and atoms in the amino acids itself. The command that i have try are: 1. info distmat (protein & sideonly) | :dex ::num_distance< 4 2. info distmat (protein & sideonly) | :dex 3. info distmat (protein & sideonly) & (:dex) distance < 4 Hope you could help me with this. Regards with thanks, Aida.

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Atoms command spec
by NUR AIDA SAKINAH 27 Sep '24

27 Sep '24

Hi ChimeraX teams, Can you guide me to use the *atoms-spec* for info distmat command. I want the output in the chimerax log to list out distances between *the drug compound and the amino acids side chains and only display the distances below than 4A*. For now, what I have got, the output includes distances between atoms in the drug itself and atoms in the amino acids itself and I don't want that. Only display distances between atoms of the drug and the amino acids side chains. The protein and drug details: PDBID= *4YVP* with drug compound *DEX* The drug binding site distance is below than *4A*. The command that i have try are: 1. info distmat (protein & sideonly) | :dex ::num_distance< 4 2. info distmat (protein & sideonly) | :dex 3. info distmat (protein & sideonly) & (:dex) distance < 4 Hope you could help me with this. Regards with thanks, Aida.

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How to increase the font size of pseudobond labels
by Suhas Srinivasan 26 Sep '24

26 Sep '24

Dear ChimeraX Community, I was trying to increase the default font size of the very small labels displayed on the pseudobonds that are generated from the “distance” command. Selecting the pseudobond label and then using the command “label size 512” had no effect. Your help would be appreciated and thank you for your time. UCSF ChimeraX 1.8 macOS 14.7

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ChimeraX download problem
by Sophie Scobell 25 Sep '24

25 Sep '24

Hi, I've been trying to download ChimeraX on my personal computer for the past two weeks and keep getting this error message: "Internal Server Error The server encountered an internal error or misconfiguration and was unable to complete your request. Please contact the server administrator at root@localhost to inform them of the time this error occurred, and the actions you performed just before this error. More information about this error may be available in the server error log." I'm using a Mac and I've tried the MacOS download on both Safari and Chrome with the same issue. Any advice would be greatly appreciated, Thank you! Sophie

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Re: Inquiry: Selecting Individual Electron Density Maps for Comparative Analysis
by Tom Goddard 25 Sep '24

25 Sep '24

Hi Yan, PDB 4ola is an X-ray structure so you could fetch PDB and the X-ray map (from the Electron Density Server) using ChimeraX commands open 4ola open 4ola from EDS The map is a unit cell and does not cover the PDB atom coordinates. To use the crystal symmetry to extend the map to cover the atom coordinates use ChimeraX command volume cover #2 atomBox #1 The x-ray map of course has other copies of the molecules packed together and if you want to see just the x-ray density near the atom coordinates you could use volume zone #3 near #1 range 3 For PDB 7sva which is a cryoEM structure with map at the EMDB with id 25446 you can open both with open 7sva open 25446 from emdb Converting the PDB files to maps gives a different result than looking at experimental results, and I'm not sure why you want to do that. But the ChimeraX molmap command will do that by adding up Gaussians at the atom positions. That does not give a good approximation to the experimental maps in most cases. All these commands are fully documented in the ChimeraX User Guide. Tom > On Sep 25, 2024, at 1:54 AM, Yan ZHANG 张艳 <zhangyan30(a)westlake.edu.cn> wrote: > > Hi Tom, > > Thank you for your response. I'll try to explain my situation more clearly. > > I am comparing two structures (PDB IDs: 4ola and 7sva). I want to use the "color near atoms" feature in ChimeraX to color the maps of both structures. However, 4ola is a crystal structure and is in MTZ format. I would like to display it in the same way as an MRC file. > > I hope this is clearer. My current solution is to convert the PDB file of 4ola to an MRC file directly. This approach seems to work, but I am unsure if it is acceptable. > > Thank you for your help. > > Best regards, > Yan > > 发件人: Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> > 日期: 星期三, 2024年9月25日 14:16 > 收件人: Yan ZHANG 张艳 <zhangyan30(a)westlake.edu.cn <mailto:zhangyan30@westlake.edu.cn>> > 抄送: chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> > 主题: Re: [chimerax-users] Inquiry: Selecting Individual Electron Density Maps for Comparative Analysis > > You don't often get email from goddard(a)sonic.net <mailto:goddard@sonic.net>. Learn why this is important <https://aka.ms/LearnAboutSenderIdentification> > Hi Yan, > > We might have advice if you can explain what you are doing more clearly. MRC files are real space maps and MTZ files contain Fourier space coefficients. > > Tom > > > On Sep 24, 2024, at 9:57 PM, Yan ZHANG 张艳 via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: > > > Dear ChimeraX Team, > > I hope this message finds you well. > > I am writing to inquire whether it is possible to selectively choose individual electron density maps of a single model from the MTZ files containing crystallographic data. This capability would enable me to perform comparative analyses of the same structure obtained through different methods. Currently, I am facing a challenge as the MRC files cannot be aligned with the MTZ files. I am seeking your guidance on whether there is a solution or tool within ChimeraX that can assist me in this process. > > Your expertise and support in this matter would be greatly appreciated. I am looking forward to hearing from you at your earliest convenience. Thank you very much for your attention to this inquiry. > > Best regards, > > Yan Zhang > Westlake University > Email: zhangyan30(a)westlake.edu.cn <mailto:zhangyan30@westlake.edu.cn> > > > > _______________________________________________ > 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

Ball representation for protein-ligand system
by Enrico Martinez 25 Sep '24

25 Sep '24

Dear ChimeraX users ! I've just found a small bug in the protein-ligand representation. if I try to change the representation of ball and sticks using: style protein ball size protein ballScale 0.18 it changes the ball representation for the both protein and ligand (e.g. defined as :lig in the system). While there is not problems with sticks: size protein stickRadius 0.12 size :lig stickRadius 0.18 So it can be applied selectively on the both selections Many thanks in advance for any suggestions ! Enrico

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Inquiry: Selecting Individual Electron Density Maps for Comparative Analysis
by Yan ZHANG 张艳 24 Sep '24

24 Sep '24

Dear ChimeraX Team, I hope this message finds you well. I am writing to inquire whether it is possible to selectively choose individual electron density maps of a single model from the MTZ files containing crystallographic data. This capability would enable me to perform comparative analyses of the same structure obtained through different methods. Currently, I am facing a challenge as the MRC files cannot be aligned with the MTZ files. I am seeking your guidance on whether there is a solution or tool within ChimeraX that can assist me in this process. Your expertise and support in this matter would be greatly appreciated. I am looking forward to hearing from you at your earliest convenience. Thank you very much for your attention to this inquiry. Best regards, Yan Zhang Westlake University Email: zhangyan30(a)westlake.edu.cn<mailto:zhangyan30@westlake.edu.cn>

2 1

Apply the user's rotation in Python
by Roden Deng Luo 24 Sep '24

24 Sep '24

Hi, If I open a protein structure, change the right mouse to rotate, select the structure, rotate it by the right mouse, and then execute the following script in the Python Shell, the structure will be moved; see the video ( https://i.gyazo.com/d72344f9c8610298f574c23e53224aac.mp4) I would expect it to be not moved as the mol.atoms.coords have not been changed. The mol.atoms.scene_coords have been changed instead. But this could be my misunderstanding of the design intent. I encounter some bugs in the downstream analysis using scene_coords only. from chimerax.atomic import Structure mol = session.models.list(type = Structure)[0] transformation = mol.scene_position mol.atoms.transform(transformation) However, if I open the same structure again and execute the following, it will go to the user's rotation. mol_2 = session.models.list(type = Structure)[1] mol_2.atoms.transform(transformation) So, I then applied the following code in my script. As a result, everything is as expected, and there is no bug. mol_path = mol.filename transformation = mol.scene_position mol.delete() mol = run(self.session, f"open {mol_path}")[0] mol.atoms.transform(transformation) I wonder if there is a way to bypass this re-opening of the file. I am with version 1.7.1 (2024-01-23) on Win 11. Many thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Bond built manually with ChimeraX not shown up in Coot
by Kai Cai 24 Sep '24

24 Sep '24

Dear colleagues, I am trying to build a N-glycan into my model using 'bond' command with ChimeraX, by connecting the ND2 atom from an ASN residue to the C1 atom of the N-glycan (NAG). However, the manually built bond didn't show up when I opened the coordinates in Coot. Is there a way to overcome this issue? The bond length is 1.4 Å. Thanks in advance! Cheers, Kai ________________________________ UT Southwestern Medical Center The future of medicine, today.

2 4

unroll the helical structure
by Dmitry Semchonok 24 Sep '24

24 Sep '24

Dear colleagues, When one has a helical structure, can it be unrolled, and can the new unrolled map be saved? Thank you. Kind regards, Dmitry

2 1

Question about processing of multi-model PDB
by Enrico Martinez 23 Sep '24

23 Sep '24

Dear Chimera-X users ! I am working on the processing of a multi-model pdb file containing biological assembly of the dimeric protein. Precisely, every monomer is in a separate model with the same chain ID (A). I need to rename the chain A to chain B in the second model and then fuse the both models, so that the entire construction will be in the same model. What commands could be used to such modifications? Many thanks in advance Enrico

2 3

Identify Contacts?
by Shawn Rumrill 23 Sep '24

23 Sep '24

Hello ChimeraX Users, I would like to analyze protein/nucleic acid complexes from the PDB by comparing the protein/nucleic acid chain interactions in each. Ideally I would like to know: * The number of interactions < 4.0 A that the nucleic acid makes with neighboring protein chains * If possible, output a list of those interactions to a text file * Even better, generate a 2D interaction map I tried contacts (#1/A | #1/B) #1/C cutoff 4.0 saveFile contacts_ABC.txt for the first bullet (with a few permutations when it didn't work), but received the error "expected a keyword." Has anyone successfully determined something like this in ChimeraX? Thanks for the input! Shawn R Rutgers University

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Re: [Chimera-users] Generating a single electrostatic potential surface for a protein + ligand complex
by Elaine Meng 22 Sep '24

22 Sep '24

Hi Jade, This chimera-users email address is for questions about Chimera. In the future, for questions about ChimeraX, please instead use the other address chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (CC'd on this message) to avoid confusing other users. This answer is for ChimeraX and does not apply to Chimera: If you meant you wanted a single surface that goes around both the ligand and the protein in a single blob: You would have to use the "surface" command with the "include" option to make a single surface around both the ligand and the protein. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/surface.html#options> Then you would have to use "coulombic" command with the "surfaces" option to use the surface you already made instead of one that has the protein only. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coulombic.html#charges> Example commands for PDB file 8iyx with GPR34 receptor with antagonist bound, residue name S6R. This example assumes you want to see the potential that is from both the receptor and the ligand, on the surface that is both the receptor and the ligand. open 8iyx surface include protein | :S6R coulombic protein | :S6R surfaces #1.2 The surface command says to make a single blob around both protein and residue S6R (the symbol between them is a vertical bar character). The coulombic command says to calculate the electrostatics using the charges of both the protein and residue S6R, and use it to color the previously made surface #1.2. You have to look in the Models panel and use the disclosure triangle to see what model number the surface has. 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 Sep 21, 2024, at 11:07 PM, jadeshi88--- via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > New user to ChimeraX here, would really appreciate some help! > > I'm trying to generate an electrostatic potential surface for a protein-ligand complex. Currently, I am using the surface/coulombic, and surface ligand/coulombic ligand commands to generate surfaces separately for the protein and ligand, and then exporting to an .obj file. However, by doing so I'm left with two separate surface meshes, and what I really want is a single surface that encapsulates both entities. Is it possible to do this? > > Thanks in advance!

2 1

Transition of the camera between two view perspectives
by Enrico Martinez 22 Sep '24

22 Sep '24

Dear Chimera-X users ! I have a question about the transition of the camera between two different views. E.g. I have (1) a closed zoom view on some selection with the defined coordinates view matrix camera 0.33173,-0.24137,-0.91197,-114.7,0.22734,0.95868,-0.17103,31.486,0.91557,-0.15059,0.3729,66.518 and (2) some general view of the whole system, with the same coordinates. Now, starting from the closed view I need to gradually move camera from (1) to the (2), which can be manually achieved using move command e.g. # zoom out and shift camera to the right move z -0.3 300; move y -0.05 300 Would it be possible additionally to provide coordinates of the both views in order to make such a camera transition more smooth and accurate ? Many thanks in advance ! Enrico

2 3

Ligand protein interaction in visual
by Mamadou Sangare 22 Sep '24

22 Sep '24

Dear I would like to insert in my PPT presentation ten ligands (chemical compounds) interacting with the binding site of the protein with chimera X. Thank you in advance for your support Kind regards! Mamadou SANGARE, PhD student ACE-Mali

2 1

Slight bug in ChimeraX
by Sergio Pipaón Alcíbar 19 Sep '24

19 Sep '24

Hello!! My name is Sergio Pipaón, from the National Center for Biotechnology in Madrid. I wanted to report a couple of -what I believe are- bugs: 1) I hate the depthCue to visualize my structures, so I usually run: lighting depthCue false in my sessions. However, for some reason, this is not stored in the session info, and you have to run it again every time you close and open your session. 2) The commands that you can introduce in the ’Startup’ section of the preferences seem to not work in some cases (I am referring to the ‘Execute these commands at startup’ text box). The aliases work fine, but I also have written the following: graphics silhouettes true lighting soft lighting shadows true lighting depthCue false ~cofr And these do not seem to run. Definitely not the lighting depthCue false. Extra: I would be cool to have a button in ‘Graphics’ to easily change the depthCue from to true to false. Am I obsessed with the depthCue? Maybe, but I hope that this is valuable feedback. I am currently running ChimeraX-1.8-rc2024.05.10. Thank you guys!! Sergio. -- Sergio Pipaón Alcíbar (PhD Student) Dept. of Macromolecular Structures, lab. S0 / Ext: 5347 National Center for Biotechnology (CNB - CSIC) C/ Darwin, 3 28049, Cantoblanco-Madrid email: spipaon(a)cnb.csic.es

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Re: [Chimera-users] Selecting chain via command line
by Elaine Meng 19 Sep '24

19 Sep '24

Hi Ellen, You sent this question to the Chimera address -- in the future, please send ChimeraX questions to the ChimeraX address chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> CC'd here to avoid confusing the other users. This answer is for ChimeraX: It works for me: labels show the insertion code. Make sure you have ChimeraX 1.8 or newer. Example 1h4w which has residues with insertion codes 184A, 188A, 221A: open 1h4w label :184,184A height 2 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 Sep 17, 2024, at 10:20 PM, Ellen Shrock via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine and Eric, > > I hope all is well. I am writing because I am using the chimerax command 'label sel residues height 1' but I noticed that the insertion codes are not making it into the labels. I attached an example cxc session along with the commands provided. In, for example, model #4, there are two residues labeled '100' even though when I hover over the residues, they have insertion codes. Do you know if there is a way I can label the residues with the position numbers including the insertion codes? > (I copied below the entire script I ran. Please let me know if there is any additional information I can provide.) > > Thanks, > Ellen > >

2 1

Displaying methyl groups on DNA?
by Maja Divjak 18 Sep '24

18 Sep '24

Hi there, Hope you're well. I'm sure this is a rookie question, but I'm having trouble displaying the methyl groups on a methylated DNA sequence, as shown in PDB 6C1Y. [A colorful structure with multiple colors Description automatically generated with medium confidence] I've tried selecting the DNA and then showing the methyl functional group, but this selects all the methyl groups including those in the protein sequence. I also tried selecting the individual bases I know are methylated using eg select #2/C:6, but not sure of the command to show the methyl group following this ie select #2/C:6 show methyl does not work, whereas show methyl as a solo command shows all methyl groups in the whole structure. Couldn't find anything in the help files, unfortunately. Thanks so much and best wishes, Maja

2 2

(no subject)
by Kasia Ojar 18 Sep '24

18 Sep '24

Hello, I hope this email finds you well. I am writing because I have a couple of questions regarding opening up the ChimeraX program. I am a student and I have downloaded the ChimeraX and cannot seem to open the program despite it being on my desktop. I have Microsoft and the software is Windows 11. Thank you for your help.

2 1

Missing libraries from package install ChimeraX?
by Mike King 17 Sep '24

17 Sep '24

Hi I have just installed ChimeraX 1.8 from the RedHat 8 rpm package. In our previous Chimera installs there were some libraries that don't appear to be in the 1.8 rpm distribution. For example, _multiscale.so and _chimera.so which our developers have been using, are these available via a different route for ChimeraX 1.8? Many thanks Mike Mike King Director, Scientific Computing Astex Pharmaceuticals 436 Cambridge Science Park Milton Road, Cambridge CB4 0QA, UK Tel: +44(0)1223 435095 Email: mike.king(a)astx.com Website: http://www.astx.com<http://www.astx.com/> This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately.

2 1

MD
by SAWABE Tomoo 17 Sep '24

17 Sep '24

To whom it may be concerned, Thank you so much for developing excellent program for analyzing protein structures. I found Chimera could do molecular dynamics simulations. If I do MD to predict proton paths described in https://www.pnas.org/doi/epdf/10.1073/pnas.1706278114, please teach me which tool we can use. Best Tomoo Sawabe Hokkaido Univ.

2 2

Error when opening session file cross-platform
by Alexander Lee 17 Sep '24

17 Sep '24

I created a python session file on ubuntu and tried to open it on windows. Ubuntu was using Chimera 1.18 build 42535 but windows was using 1.18 build 42531. I've tried updating chimera on windows, but it said I was on the latest version already. When I open it on ubuntu, it works. My session file is ~ 1.5 GB including smoothed trajectory. What should I do? Here are the outputs after running debug on windows: Cannot execute 'gzip': no automatic decompression of .Z files initializing general preferences loading Tix initializing graphics create application loading Pmw creating main window creating menus creating toolbar creating viewer initializing OpenGL initializing preferences initializing dialogs initializing COM initializing extensions Return code: -1073741819 Press return or enter to to exit [cid:0c988132-7bb8-429c-a6c7-f91f6db3b590] [cid:55bba9bf-1168-4782-b772-4d2e36e05e97]

1 0

Change fetch download location
by Walker Orr 13 Sep '24

13 Sep '24

Hi, I was wondering how to change the fetch download location from downloads to a custom-assigned folder. I saw how to do this on chimera, but couldn't find guidance for ChimeraX in the documentation. Is there a way to do this? Thanks, Walker

2 1

Molmap default to cubic box?
by Oliver Clarke 13 Sep '24

13 Sep '24

Hi, Currently, molmap defaults to creating the new map in a minimal bounding box - a minimal rectangular prism. Most cryoEM software doesn't like rectangular prisms, and rather prefers cubes (ideally with sides that are an even number of voxels). Would it be possible to either (a) alter molmap so it defaults to a minimal cubic box or (b) add an option to automatically resample to a cubic box of specified dimensions? Often this doesn't really matter as we have a map already loaded that we can resample on the grid of, but it would be convenient to be able to do this in a single command. Cheers Oli

3 5

Save Session
by F.Xavier Gomis-Rüth 12 Sep '24

12 Sep '24

Dear Elaine, I am trying to save the session under ChimeraX v. 1.8 but the program refuses to do so with the message below. Any suggestion is welcomed. Best, Xavier --

2 2

Chimerax's download link is no longer working
by 卢健之 11 Sep '24

11 Sep '24

Hello, I tried to dowonload the chimerax from the link https://www.rbvi.ucsf.edu/chimerax/download.html. But it seems the server is down. I wonder if you could provide me with a new download link. I would really appreciate it.

2 1

no template at MD forcefield
by Dmitry Semchonok 11 Sep '24

11 Sep '24

Dear Tristan and colleagues, I hope you are doing well. I have a question about the cofactors and residues that ISOLDE cannot see immediately. [cid:17de3c4d-4ac6-471b-b5b9-ecaa4e534d18] What is the proper way to treat them? The program proposes that I do a search and then give the options. Shall I select the most probable one out of the list? And how do we deal with Chlorophylls (Chl a; Chl b) and carotenoids (car)? And sometimes, even with regular ones like ARG [cid:8ff9222b-feb1-47b3-9b5e-a52e714e2355] Thank you in advance. Kind regards, Dmitry

2 1

Select all connected atoms to selection
by Alexander Lee 10 Sep '24

10 Sep '24

Hi! I want to select all covalently bonded atoms to my selected atom. Is this possible? Currently, I'm using the command select @{atom_name}; select zone select 2 It works, but I'm worried about accidentally catching any stray unconnected atoms when doing this in batches of pdbs. Thanks!

3 2

atoms.scene_coords inconsistency before and after saving
by Roden Deng Luo 10 Sep '24

10 Sep '24

Hi, With version 1.7.1 (2024-01-23), if I open a structure (tested with 6MEO and 6ARA), select the whole molecule, change "Right Mouse" to "Rotate model", rotate the model by dragging with the right mouse, save the model into a .cif file (uncheck "Use untransformed coordinates"), and then type the following python script in the Shell in the session performed the rotation and in a new session/launch of ChimeraX and opening of the saved file, the results are different, see the attached screenshots. ======= from chimerax.atomic import Structure mol = session.models.list(type = Structure)[0] mol.atoms.scene_coords ======= For 6ARA, if I do not change the camera setting before rotation (drag the left mouse), only rotate in the original camera setting, this is not reproduced. But if I change the camera setting, this is reproduced. For 6MEO, I always reproduce the described behavior. From https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/atomic/atomic.html#chi… , *property *scene_coords <https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/atomic/atomic.html#chi…> Atoms’ coordinates in the global scene coordinate system. This accounts for the Drawing positions for the hierarchy of models each atom belongs to. Either I misunderstood the whole scene and camera system, or this should not have happened. Why is this the case? How can I access from the session performed the rotation the coords as in a new session? Many thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

2 2

license for university students
by Angel David Montijo Valdés 09 Sep '24

09 Sep '24

Good afternoon, I am writing to you in the kindest way to request a free use license for the chimera X program. Because I am a student at the National Autonomous University of Mexico (UNAM), within the Faculty of Sciences, and it would be a great opportunity to use your tool in different molecular biology analyses. If you need a proof of my identity as a student, you can ask me for it without any problem. I look forward to hearing from you. Best regards.

2 1

Select multiple rotamer conformations for a single amino acid
by Alexander Lee 09 Sep '24

09 Sep '24

Hi! I was able to select and use multiple rotamer conformations simultaneously for a single amino acid using the Rotamers tool, saved as alternate locations within a pdb file. Is there a way to do that using swapaa or from the command line?

2 3

Ribbon style editor
by Alessio Nocentini 09 Sep '24

09 Sep '24

Hello, I have been an academic user of chimera for years. I have just downloaded chimerax but I cannot find the ribbon style editor. Can you please help? Best regards Alessio -- Dr. Alessio Nocentini University of Florence Neurofarba Department Via Ugo Schiff 6, 50019 - Sesto Fiorentino (Firenze), Italy Phone: +39-055-4573685 *NEUROFARBA Dipartimento di **ECCELLENZA 2023-2027*

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Re: [Chimera-users] morph command in chimerax
by Elaine Meng 09 Sep '24

09 Sep '24

Hi Bryan, Since this is a ChimeraX question, I've CC'd chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> --- in the future please use that mailing list for ChimeraX questions, because we don't want to confuse users between the two programs, for which the answers may be different. This answer is for ChimeraX: The "morph" command is for atomic structures, not maps. That's why it keeps saying you need structures! This is mentioned in the first sentence of the help page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/morph.html> To instead morph maps, see the "volume morph" command: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#morph> 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 Sep 9, 2024, at 7:29 AM, Hansen, Bryan (NIH/NIAID) [E] via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi, > I’m using ChimeraX v 1.8 (2024-06-10) and I’m having a problem with the morph command. No matter how I format the command I’m getting the same error message of “Require at least 2 structures for morph” I’ve tried > morph #3,4 core 0.1 frames 75 wrap t > and > morph #3#4 core 0.1 frames 75 wrap t > These are 2 electron density maps so there’s no sequence info docked in yet. Thanks for any tips or advice on what I’m doing wrong. > Bryan Hansen

1 0

MD Trajectory
by Mcguire, Kelly 06 Sep '24

06 Sep '24

What is the largest MD trajectory file (i.e. DCD) ChimeraX can handle? VMD is designed for very large MD trajectory visualization and analysis. Is ChimeraX for smaller trajectories? Kelly McGuire PhD Postdoc - Herzik Lab University of California - San Diego

2 1

colored stl file for 3d printing
by Haydar Witwit 06 Sep '24

06 Sep '24

Dear ChimeraX team, I'd like to know if it is possible to save a colored file of pdb into stl, because when I save the file as stl, chemierax saves it as a monocolor structure. Actually, my intention was to 3d print a hydrophobic structure of small protein but labeled with one letter code label and position of the amino acids. Something similar to the following image: [cid:4c34bc91-300a-456c-8583-ab4de7f1b1d9] Kind regards Haydar

2 1

Re: Optimizing ChimeraX Performance for Multiple Subtomo Maps
by Tom Goddard 06 Sep '24

06 Sep '24

Hi Wang, Glad to hear ArtiaX helps showing your subtomogram averaged particles. An important feature of that extension written by Utz Ermel optimizes the display of thousands of particles by not using a separate ChimeraX model for each one. I tried opening 1500 maps of size 20 x 20 x 20 grid points in ChimeraX 1.8 on a Mac Studio M2 Ultra with much less powerful graphics than an Nvidia 4090, displaying all as surfaces, full lighting, and they rotated, zoomed and translated usably fast at 9 frames per second. So I am surprised you had a problem and I don't know why it is slow for you. Tom > On Sep 6, 2024, at 3:01 AM, 王光磊 <wangguanglei20(a)mails.ucas.ac.cn> wrote: > > Hi Tom, > > > Thank you for your prompt response. > > It seems that the performance issue was caused by the excessive number of subtomo maps. In my case, I loaded approximately 1,500 subtomo maps using the subtomo2chimera script, and displayed them in surface mode. This led to ChimeraX freezing for several seconds after any rotation or zoom of the view. Loading an extra tomograph did not affect performance. > > I tried using AriaX to load the subtomo maps, and now the scene runs smoothly. Thank you for your advice! > > Thanks, > > Wang GuangLei > > > > -----原始邮件----- > 发件人:"Tom Goddard" <goddard(a)sonic.net> > 发送时间:2024-09-06 03:34:59 (星期五) > 收件人: 王光磊 <wangguanglei20(a)mails.ucas.ac.cn> > 抄送: chimerax-users(a)cgl.ucsf.edu > 主题: Re: [chimerax-users] Optimizing ChimeraX Performance for Multiple Subtomo Maps > > Hi Wang, > > I think your Nvidia 4090 should handle the large tomogram fine, and probably the slowdown is because having 1000-2000 open model of any kind, even if they are small like your subtomo maps, is more than ChimeraX was designed to handle. I am surprised though that rotating the view becomes slow because that should just move the camera which should not depend on the number of models shown. Do I understand correctly that you just open the tomogram and 1000-2000 subtomograms, display them all, and rotate and it updates slowly? How slowly, like 1 frame per second, or does it freeze for ten seconds? What display style do you use for the subtomograms, surface or volumetric? > > You might be interested in the ArtiaX ChimeraX extension which is for looking at particles in tomograms. You would get it using ChimeraX menu Tools / More Tools.... > > Tom > > >> On Sep 5, 2024, at 1:15 AM, 王光磊 via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> >> >> Hi, >> >> I'm using chimerax to display my tomograph and multiple subtomo averages in surface mode. Specifically, I need to visualize a 1440*1022*250 tomograph, along with 1000-2000 subtomo maps, sized at 32x32x32 and 16x16x16. However, loading such a large number of maps has significantly slowed down ChimeraX, particularly when rotating the view. Is there any settings to improve interactive performance or increase hardware utilization? I hope to avoid cropping the tomograph. >> >> My system specifications are as follows: >> >> Dual Intel Xeon 5317 processors(a)3.00GHz >> RTX 4090 GPU >> 128GB RAM >> Operating System: CentOS Stream 9 >> GNOME Version: 40.4 >> GPU Driver Version: 550.54.15 >> I would greatly appreciate any suggestions. >> >> Thanks, >> >> Wang GuangLei >> >> _______________________________________________ >> 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

error in the documentation?
by Bourguet,Pierre 06 Sep '24

06 Sep '24

Dear ChimeraX support, First of all, thank you for developing & maintaining such an easy-to-use software. I am not trained as a structural biologist, but I looking at more and more structures thanks to alphafold. The journey is much nicer since I switched to ChimeraX! I have noticed the following inconsistency in the documentation. https://rbvi.ucsf.edu/chimerax/docs/user/commands/alphafold.html#contacts "If one set of entities is higher-confidence (lower in pLDDT<https://alphafold.ebi.ac.uk/faq#faq-12>) than the other, it is usually best to specify them as the aligned set so that the coloring will show the error values of the lower-confidence set." My understanding is that it should say "(higher in pLDDT)". Hopefully that helps! Best, Pierre Pierre Bourguet Postdoc Gregor Mendel Institute of Molecular Plant Biology GmbH Dr. Bohr-Gasse 3, 1030 Vienna, Austria pierre.bourguet(a)gmi.oeaw.ac.at http://www.gmi.oeaw.ac.at [cid:gmi_48f983b7-0679-4d21-99bc-bda376e5bf6b.png]

2 2

Optimizing ChimeraX Performance for Multiple Subtomo Maps
by 王光磊 05 Sep '24

05 Sep '24

Hi, I'm using chimerax to display my tomograph and multiple subtomo averages in surface mode. Specifically, I need to visualize a 1440*1022*250 tomograph, along with 1000-2000 subtomo maps, sized at 32x32x32 and 16x16x16. However, loading such a large number of maps has significantly slowed down ChimeraX, particularly when rotating the view. Is there any settings to improve interactive performance or increase hardware utilization? I hope to avoid cropping the tomograph. My system specifications are as follows: Dual Intel Xeon 5317 processors(a)3.00GHz RTX 4090 GPU 128GB RAM Operating System: CentOS Stream 9 GNOME Version: 40.4 GPU Driver Version: 550.54.15 I would greatly appreciate any suggestions. Thanks, Wang GuangLei

2 1

Discrepancy: plDDT laphafold3 and ChimeraX version 1.9.dev202405310031 (2024-05-31)
by Khawar Siddiqui 03 Sep '24

03 Sep '24

Dear Tom and ChimeraX team I recently did some protein structures using AF3. I found that the plDDT color prediction given by AF3 differs from when I opened the downloaded file in ChimeraX. Both photos are below. Can you please guide me to where I am making the mistake? Some adjustments may be needed. The AF3 coloring (right) shows prominently Blue-cyan (70-90% confidence) whereas after opening the same file in ChimeraX (left) shows many regions as yellow (50% confidence). Thanks again for the help. sohail Dr Khawar Sohail Siddiqui, [cid:3f847f24-9a1b-47bc-bb56-1704e8bd8ac3] [cid:2c952f1f-e76e-458e-a444-8242f6bdab3a] [cid:0089dce1-a9be-4009-93b9-d158c31cee29]hoo.com

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I found that the phosphodiester bond has broken.
by Yan ZHANG 张艳 03 Sep '24

03 Sep '24

Dear ChimeraX Team, I am writing this letter due to an issue I have encountered. I have adjusted the phosphodiester bonds of the RNA chain using Coot for structure correction. However, when I opened it in ChimeraX, it appears to be in a broken state, even though the distance between the two atoms is 1.6 angstroms. I am unsure what the reason for this could be. I have attached an image below. The dashed line should originally be a P-O bond. Could you please suggest any solutions to this problem? I look forward to receiving your reply as soon as possible. [cid:image001.png@01DAFDEC.77532DA0]

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Purchase license
by Lili Ye 03 Sep '24

03 Sep '24

Hello, I am from Sironax(Beijing)Co.,Ltd. We want to buy two licenses now, how to buy? Thanks! Lili Ye 叶丽丽 Sironax (Beijing) Co., Ltd. 维泰瑞隆（北京）生物科技有限公司 Add: Building 2, No.9 Yike Road, Zhong-Guan-Cun Life Science Park, Changping district, Beijing, China 102206 北京市昌平区生命科学园医科路9号院2号楼8层 Tel: （+86）15201581663 Email: Lili.Ye(a)sironax.com<mailto:Lili.Ye@sironax.com> [1534753277(1)]

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Inquiry About Building Molecular Structures in ChimeraX
by 化工化工 02 Sep '24

02 Sep '24

Dear Professor, I hope this message finds you well. I am currently engaged in machine learning research using ChimeraX. As part of my work, I need to substitute various groups on the phosphorus atom, including methyl, tert-butyl, cyano groups, and others. However, the current substitution function does not cover many groups, so I have been manually adding them to the SEQCROW library. At present, I am building the structures in Gaussian, which is quite cumbersome. Since I am not very familiar with ChimeraX, I am unsure whether it allows for manual molecular structure building. If such functionality is available, it would greatly assist my work. I would greatly appreciate any guidance or suggestions you might have. Thank you very much for your time and assistance. Best regards, Youcai Zhu 化工化工 1366924572(a)qq.com  

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Re: color bfactor by alphafold palette
by Elaine Meng 02 Sep '24

02 Sep '24

To summarize for users, the ChimeraX alphafold coloring to show pLDDT values is continuously shaded, whereas the coloring shown at the AlphaFold database is similar but discontinuous, and differences may be evident. The reasoning behind the ChimeraX alphafold coloring palette is that it may be more informative about the specific values. However, it may be confusing that it looks similar, yet not the same, as the AlphaFold database pLDDT coloring. A few months ago, Abnieszka Obarska (thank you!) helpfully provided a command to match the coloring shown at the AlphaFold database. Since it was in an image, however, it is not convenient for cut and paste, so I have copied it here: color bfactor palette 0,#FF7D45:50,#FF7D45:50.00001,#FFDB13:70,#FFDB13:70.00001,#65CBF3:90,#65CBF3:90.00001,#0053D6:100,#0053D6 Although I did not check if the color hex codes exactly match the AlphaFold database colors, I tried it on a couple of examples at least to my eye, it reproduced the coloring of structures shown at the database. 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

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AlphaFold PAE plot not generated
by Catrin McHugh 30 Aug '24

30 Aug '24

Good morning Having successfully generated a PAE plot (and coloured the model accordingly) with data generated by AF3, I am getting an error message when I try to do the same using a JSON file generated by ColabFold for AF2. The error message is: 'is not AlphaFold predicted aligned error data, expected a top level list". I attach the JSON file, and the relevant structure PDB. Many thanks in advance Catrin

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Random residue colors?
by Daniel Asarnow 30 Aug '24

30 Aug '24

Hi all, In the color command documentation, it says 'color random' can per atom or per residue. How can random residue colors be specified? I can only get random atom colors. Thanks! -da

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CIMERAX 64BIT FOR WIN 10
by Lee, Yong Sok (NIH/NIAID) [E] 29 Aug '24

29 Aug '24

I AM LOOKING A FOR A 64BIT VERSION OF CHIMERAX FOR WINDOWS 10. TRED DOWLOANDING AND INSTALLING CHIMERAX 1.8 BUT IT WOULD NOT LAUNCH ON MY WINDOWS 10 64 BIT SYSTEM. LET ME KNOW IF YOU HAVE A SOLUTION FOR THIS ISUUE. LOOKING FORWARD TO HEARING FROM YOU.

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Invitation to conduct a UCSF Chimera Workshop at Purdue University
by Ferdausi, Nourin 29 Aug '24

29 Aug '24

Dear Team, I hope this email finds you well. My name is Nourin Ferdausi and I am a graduate student at the Department of Biological Sciences in Purdue University. My colleague, Priyanka Naik (cc’d here) and I are writing to you on behalf of the Structural Biology and Biophysics Club (SBBC). We are hoping to organize a virtual workshop focused on UCSF Chimera, and we would be honored if one of your team members could conduct this workshop. The graduate students and researchers of our structural biology group use a wide variety of experimental approaches like cryo-electron microscopy and X-ray crystallography for determining molecular structures. Consequently, the Chimera software is integral to our research, and we believe your insights would be of great impact to our community. We are flexible with the format of this virtual workshop, which is tentatively scheduled for mid-September; however, we are open to adjusting the date based on your availability. Your participation will provide our members with a unique opportunity to learn directly from a developer of UCSF Chimera. Please let me know if we can have a quick Zoom call to discuss the event in detail. We look forward to your reply at your earliest convenience! Thank you, Nourin Ferdausi Ph.D. Candidate, Noinaj Lab Supporting officer, Structural Biology and Biophysics Club Department of Biological Sciences Purdue University Hockmeyer Hall of Structural Biology West Lafayette, IN-47907-2054

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Re: [Chimera-users] Finding SASA for individual residues
by Elaine Meng 29 Aug '24

29 Aug '24

Hi Ale, In the future please use chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (CC'd here) for ChimeraX questions. This chimera-users@cgl address is for Chimera, which is a different program, and I don't want to confuse the other users. Everybody, this answer is for ChimeraX: I believe you are misunderstanding how "measure sasa" works. It will actually enclose the specified atoms in a surface, so if you say "measure sasa :12" that surface will only be around residue 12 and ignore all the other atoms. I am guessing that you really want the SASA of the aromatic rings in the context of the surface that goes around the whole protein, not for a bunch of individual bubbles drawn around each aromatic ring. In that case, your commands are wrong. Instead you want something like: measure sasa protein sum :trp,tyr,phe & aromatic-ring See "measure sasa" help for description of how it works: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> 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 Aug 29, 2024, at 4:16 AM, alessandro.strofaldi--- via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > > I'll reply to this post for my question cause the title seems appropriate. > I've a one-chain protein and I simply want to calculate the SASA of the aromatic-ring of all TRP,TYR and PHE of the protein using ChimeraX. > > This is the log: > measure sasa /A > Solvent accessible area for /A = 22276 > measure sasa /A:trp & aromatic-ring > Solvent accessible area for /A:trp & aromatic-ring = 1824.9 > measure sasa /A:phe & aromatic-ring > Solvent accessible area for /A:phe & aromatic-ring = 3339.6 > measure sasa /A:tyr & aromatic-ring > Solvent accessible area for /A:tyr & aromatic-ring = 3977.3 > > But the I tried to get the sum: > > measure sasa /A:trp,tyr,phe & aromatic-ring sum :trp,tyr,phe > Solvent accessible area for /A:trp,tyr,phe & aromatic-ring = 7683.3 > Solvent accessible area for :trp,tyr,phe (285 atoms) of /A:trp,tyr,phe & aromatic-ring = 7683.3 > > Which is different from the sum of the values I got before. I think I'm missing something basic on SASA calculations... > Also, from your answer to Prathvi, those numbers should be squared Agstrom. Do these number make sense? For a single residue (measure sasa:263, which is a surface-exposed Tyrosine) I got 331.95. Those values are similar to what Prathvi got so am I doing the same mistake? I was expecting, for a single residue something like two order of magnitude less. > You said ".. then it will make a surface that only encloses that one residue, with area 292 as you said. I'm pretty sure that is NOT what you want. Instead you want tthe surface of the whole protein (or maybe one chain) and then the area of the residue given that larger surface. " Does this means that with the commands I typed ChimeraX "Isolates" the residue and calculate the SASA as if it was not included in the protein? > Anyway, I think it is clear I'm an unexpert user so If there is any tutorial about SASA on ChimeraX (could not find those, only for Chimera), please, feel free to suggest. > > Thank you!! > Best, > Ale

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Re: Command line interface saving
by Mark Rosenberg 26 Aug '24

26 Aug '24

Thanks, Guillaume, for the excellent service. I found the log window now. I cannot cycle through my previous commands, though; in the bottom window, “command:’ with the down and up arrow. Is there a way to import those, please? Many thanks Mark mjfssmr mark.rosenberg(a)manchester.ac.uk<mailto:mark.rosenberg@manchester.ac.uk> mjfssmr mark.rosenberg(a)manchester.ac.uk<mailto:mark.rosenberg@manchester.ac.uk>mjfssmr mark.rosenberg(a)manchester.ac.uk On 26 Aug 2024, at 12:46, mjfssmr <http://mark.rosenberg@manchester.ac.uk> wrote: Thanks, Guillaume, for the excellent service. I found the log window now. I cannot cycle through my previous commands, though; in the bottom window, “command:’ with the down and up arrow. Is there a way to import those, please? Many thanks Mark mjfssmr mark.rosenberg(a)manchester.ac.uk mjfssmr mark.rosenberg(a)manchester.ac.uk On 26 Aug 2024, at 12:31, Guillaume Gaullier <http://guillaume.gaullier@KEMI.UU.SE> wrote: Hello, The log of your saved session should be there, but it is hidden at the top of the log window when you re-open the session file. There should be a black triangle that you can click to open the log contents from the previous session. I hope this helps, Guillaume ________________________________ From: Mark Rosenberg via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Sent: Monday, August 26, 2024 1:26:25 PM To: chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Command line interface saving Hi If I save my session in .cxs format, move to another machine, and open the same session again, I “lose" my commands. The commands don’t appear to be saved. How do I remedy this, please? Thanks Mark 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/ [http://uu.se<https://urldefense.com/v3/__http://www.uu.se/om-uu/dataskydd-personuppgifte…> 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 [http://uu.se<https://urldefense.com/v3/__http://www.uu.se/en/about-uu/data-protection-po…>

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Re: Command line interface saving
by Guillaume Gaullier 26 Aug '24

26 Aug '24

Not that I know, sorry. But maybe somebody else knows, so it is better to keep the list in CC. 😊 Cheers, Guillaume ________________________________ From: Mark Rosenberg <mark.rosenberg(a)manchester.ac.uk> Sent: Monday, August 26, 2024 1:46:29 PM To: Guillaume Gaullier Subject: Re: Command line interface saving Thanks, Guillaume, for the excellent service. I found the log window now. I cannot cycle through my previous commands, though; in the bottom window, “command:’ with the down and up arrow. Is there a way to import those, please? Many thanks Mark mjfssmr mark.rosenberg(a)manchester.ac.uk mjfssmr mark.rosenberg(a)manchester.ac.uk On 26 Aug 2024, at 12:31, Guillaume Gaullier <guillaume.gaullier(a)KEMI.UU.SE> wrote: Hello, The log of your saved session should be there, but it is hidden at the top of the log window when you re-open the session file. There should be a black triangle that you can click to open the log contents from the previous session. I hope this helps, Guillaume ________________________________ From: Mark Rosenberg via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Sent: Monday, August 26, 2024 1:26:25 PM To: chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Command line interface saving Hi If I save my session in .cxs format, move to another machine, and open the same session again, I “lose" my commands. The commands don’t appear to be saved. How do I remedy this, please? Thanks Mark 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/ [uu.se]<https://urldefense.com/v3/__http://www.uu.se/om-uu/dataskydd-personuppgifte…> 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 [uu.se]<https://urldefense.com/v3/__http://www.uu.se/en/about-uu/data-protection-po…> 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.

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Command line interface saving
by Mark Rosenberg 26 Aug '24

26 Aug '24

Hi If I save my session in .cxs format, move to another machine, and open the same session again, I “lose" my commands. The commands don’t appear to be saved. How do I remedy this, please? Thanks Mark

1 0

molmap command question
by Grigory Mechetin, Ph.D. 23 Aug '24

23 Aug '24

Dear ChimeraX developers, when I use the molmap command on grid ('molmap #1 10 onGrid #2', grid2 was created with' vop new size 256,256,256 gridSpacing 0.74' command ) I get half-map. How to get the full one? When I use molmap without onGrid it generates the volume with non-equal grid size, but I need square 256^3 grid. [cid:3853c8fe-0ccd-4133-ba08-4732e3be8905] Best regards, Grigory Mechetin, PhD, MEMS, Duke University.

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Data handling / privacy policy information?
by Frumolt, Brian 23 Aug '24

23 Aug '24

Hi, We are looking at ChimeraX for commercial use. I was looking on the site for information related to data use and privacy policies. I understand the app runs locally, but was wondering whether it leverages any web services, or passes any data outside the local installation? We have strict data handling policies in place for our clients, so would need to be aware. If there is a policy document I missed, that would be ideal. Thanks! Brian This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying, or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently delete the original and any copies of this email and any attachments thereto.

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Morphing two GPCR conformations
by Enrico Martinez 23 Aug '24

23 Aug '24

Dear Chimera-X users! I try to use the morph command to model the conformational change of GPCR related to its activation. Having two superimposed conformations of the receptor, which are different in the position of the internal part of the transmembrane helix VI, I try to visualize the displacement of this helix using morph #2,1 frames 250 Unfortunately the produced trajectory looks very unnatural (one helix overlaps with another one). Would it be possible to improve the accuracy of such morphing e.g. providing some restraints? Many thanks in advance ! Enrico

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Mol 2.0 desktop version
by Nicholas Koylass 22 Aug '24

22 Aug '24

Good day, I am trying to interface ChimeraX with a XML file that was converted to json to perform MOLE Channel Coloring by Property. However, I did not use the mole server. I used the desktop version since the server was unavailable. Thus, I received this error : molepore-7sqf.json does not look like Mole Online json file, does not contain Channels. Can anyone assist me with this? Thanks, Respectfully, Nicholas Nicholas Koylass Ph.D. Candidate, Department of Physiology, Qiu Lab XDBio Graduate Program Johns Hopkins School of Medicine nkoylas1(a)jh.edu

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Restoration of missing helical fragments of the structure
by Enrico Martinez 22 Aug '24

22 Aug '24

Dear Chimera-X users ! Suppose I have a pdb structure with a missed C-terminal fragment corresponding to the transmembrane helical part that should anchor the protein in the membrane. Is it possible to use some built-in utilities (modeller?) to predict this missing fragment based on the full length sequence of the entire construct? Many thanks in advance Enrico

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results swiss dock
by Aurélie Hoeffel 21 Aug '24

21 Aug '24

Dear Chimeras members, I obtained some docking results from swiss dock, unfortunately my result.dock4 document is not readable in chimerax, I did not achieve to open it. Is it something special I have to do? Because, on the website it is written that we can directly upload it and it will work but for me chimerax did not recognize my .dock4 document. What should I do? Thank for the answer, Aurelie Hoeffel

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ChimeraX docker arm64
by Daniel Diaz 20 Aug '24

20 Aug '24

We are unable to install chimerax in our ubuntu 22.04 docker image when running on arm64 architecture. We use it to add hydrogen atoms to our cif files for our protein ML data engineering pipelines. We are trying to scale our dataset generation pipeline to the new cluster on TACC (vista) which has arm64 chips. We are running it in a singularity container, which I create by converting my docker image, and I am unable to build the docker image using arm64. How do you recommend we proceed? Here is the error stack: $ apt-get update --fix-missing && apt-get install -y /dependencies/chimerax-daily.deb Hit:1 http://ports.ubuntu.com/ubuntu-ports jammy InRelease Hit:2 http://ports.ubuntu.com/ubuntu-ports jammy-updates InRelease Hit:3 http://ports.ubuntu.com/ubuntu-ports jammy-backports InRelease Hit:4 http://ports.ubuntu.com/ubuntu-ports jammy-security InRelease Reading package lists... Done Reading package lists... Done Building dependency tree... Done Reading state information... Done Note, selecting 'ucsf-chimerax-daily:amd64' instead of '/dependencies/chimerax-daily.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: ucsf-chimerax-daily:amd64 : Depends: libasound2:amd64 but it is not installable Depends: libatk1.0-0:amd64 but it is not installable Depends: libbz2-1.0:amd64 but it is not installable Depends: libc6:amd64 but it is not installable Depends: libcairo-gobject2:amd64 but it is not installable Depends: libcairo2:amd64 but it is not installable Depends: libcrypt1:amd64 but it is not installable Depends: libcups2:amd64 but it is not installable Depends: libdbus-1-3:amd64 but it is not installable Depends: libdrm2:amd64 but it is not installable Depends: libegl1:amd64 but it is not installable Depends: libexpat1:amd64 but it is not installable Depends: libffi7:amd64 but it is not installable Depends: libfftw3-single3:amd64 but it is not installable Depends: libfontconfig1:amd64 but it is not installable Depends: libfreetype6:amd64 but it is not installable Depends: libgcc-s1:amd64 but it is not installable Depends: libgdk-pixbuf2.0-0:amd64 but it is not installable Depends: libgfortran5:amd64 but it is not installable Depends: libgl1:amd64 but it is not installable Depends: libglib2.0-0:amd64 but it is not installable Depends: libglu1-mesa:amd64 but it is not installable Depends: libgstreamer-plugins-base1.0-0:amd64 but it is not installable Depends: libgstreamer1.0-0:amd64 but it is not installable Depends: libgtk-3-0:amd64 but it is not installable Depends: liblzma5:amd64 but it is not installable Depends: libncursesw6:amd64 but it is not installable Depends: libnspr4:amd64 but it is not installable Depends: libnss3:amd64 but it is not installable Depends: libopenjp2-7:amd64 but it is not installable Depends: libosmesa6:amd64 but it is not installable Depends: libpango-1.0-0:amd64 but it is not installable Depends: libpangocairo-1.0-0:amd64 but it is not installable Depends: libpulse-mainloop-glib0:amd64 but it is not installable Depends: libpulse0:amd64 but it is not installable Depends: libsqlite3-0:amd64 but it is not installable Depends: libssl3:amd64 but it is not installable Depends: libstdc++6:amd64 but it is not installable Depends: libtinfo6:amd64 but it is not installable Depends: libuuid1:amd64 but it is not installable Depends: libwayland-client0:amd64 but it is not installable Depends: libwayland-cursor0:amd64 but it is not installable Depends: libwayland-egl1:amd64 but it is not installable Depends: libwayland-server0:amd64 but it is not installable Depends: libx11-6:amd64 but it is not installable Depends: libx11-xcb1:amd64 but it is not installable Depends: libxcb-glx0:amd64 but it is not installable Depends: libxcb-icccm4:amd64 but it is not installable Depends: libxcb-image0:amd64 but it is not installable Depends: libxcb-keysyms1:amd64 but it is not installable Depends: libxcb-render-util0:amd64 but it is not installable Depends: libxcb-util1:amd64 but it is not installable Depends: libxcb-xinerama0:amd64 but it is not installable Depends: libxcb1:amd64 but it is not installable Depends: libxcomposite1:amd64 but it is not installable Depends: libxcursor1:amd64 but it is not installable Depends: libxdamage1:amd64 but it is not installable Depends: libxext6:amd64 but it is not installable Depends: libxfixes3:amd64 but it is not installable Depends: libxi6:amd64 but it is not installable Depends: libxkbcommon0:amd64 but it is not installable Depends: libxkbcommon-x11-0:amd64 but it is not installable Depends: libxrender1:amd64 but it is not installable Depends: libxtst6:amd64 but it is not installable Depends: zlib1g:amd64 but it is not installable E: Unable to correct problems, you have held broken packages. -- Danny Diaz, PhD Deep Proteins @ IFML Department of Computer Science University of Texas at Austin

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Protein backbone representation
by Alex Henley 20 Aug '24

20 Aug '24

I was wondering how I can achieve this structure representation. The papers I read cite Chimera, but I cannot figure it out. Any help is appreciated.

2 1

Per-Model Lighting Options
by ygilron＠asu.edu 20 Aug '24

20 Aug '24

I am trying to render different parts of my model in different styles. This is done to emphasize changes in a ligand's force field between different simulations. I would like every part of my model to be rendered in "full", and only change the style for my ligand so it will appear either as "flat", with or without a "silhouettes" toggled on. Is there an option to do this? I would like to just render my custom residue "DIO" in the "flat" style. As you can see from the output it is part of chain 1: " ...Non-standard residues in dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 DIO — (DIO) ..." I tried to use the following command to separately render different parts of a chain: lighting model #1:DIO flat from the console: >lighting modell #1:DIO flat Expected a keyword while selecting DIO fro the select menu and then running : lighting flat changes the style on the whole image. P.S. full output command when I loaded the molecule: open .\dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb" format pdb coordsets true Summary of feedback from opening C:\Users\yis\Desktop\Wenwei Lab\article\first_draft_figs\dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb warnings Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV ... 1997 messages similar to the above omitted dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb title: PH06_elaxed_rank_001_alphafold2_translated_100_xyz.pdbqt in water t= 0.00000 step= 0 [more info...] Chain information for dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 Chain Description ? No description available Non-standard residues in dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 DIO — (DIO) FE2 — (FE2) dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb has 1001 coordinate sets

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Thanks Elaine, Tom, Eric and team
by Artie Kushner 20 Aug '24

20 Aug '24

Apologies for an off-topic message. I'd like to express my gratitude to Elaine Meng in particular and the rest of the RVBI team who are tirelessly killing it in the Users mailing list with questions. On top of the amazing software, I appreciate the consistency, informativeness and thoughtfulness of each individual response. I learn a lot about ChimeraX and the community by reading other people's questions and answers. Thanks and kind regards from BC and Manitoba, Canada Artem

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Assistance Required: Visualizing Complete Amino Acid Residue with Cartoon Transparency in ChimeraX
by Amandeep Sharma (P24BB0001) 19 Aug '24

19 Aug '24

Dear ChimeraX users, I am reaching out for assistance with visualizing amino acid residues in ChimeraX, particularly when part of the residue is embedded within a cartoon structure representation. I am aiming to achieve a visualization similar to what is possible in PyMOL, where the complete residue is visible even when it intersects with other structural elements and adjust the transparency of the cartoon representation so that the embedded atoms of the residue can be clearly seen. I am struggling to get the desired result. To provide context and illustrate the issue, I am enclosing images of the current visualization: - *Image 1:* Shows the current state where part of the residue is obscured by the cartoon structure. - *Image 2:* Demonstrates the desired outcome where the residue is fully visible, including the embedded atoms. I am looking for a solution that combines the aspects seen in the two attached images, allowing for clear visualization of the residue and improved transparency. Thank you very much for your assistance. I look forward to your guidance on how to achieve this in ChimeraX. Best regards, Amandeep -- Amandeep Sharma PhD Student (2024-25) Dept. of Bioscience & Bioengineering Indian Institute of Technology Jodhpur Karwar 342037, Rajasthan

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Alligning a trajectory
by ygilron＠asu.edu 19 Aug '24

19 Aug '24

Hi I am new to UCSF ChimeraX, and would like to learn how to use it for visualizing trajectories. Previously, I was using pymol for this, but would like to use ChimeraX's better image rendering for a publication. I was able to load the .pdb file of my trajectory with: open <"path/to/pdb"> format pdb coord T Currently, this is the info of my file: >info 1 models #1, lambda25_trajectory_1k_res.pdb, shown 8094 atoms, 8219 bonds, 514 residues, 1 chains ( ), 100 coordsets I would like to remove translations and rotations by fitting each frame with a command similar to 'align': align matchatoms toAtoms refatoms [ cutoffDistance d ] [ move what ] [ each level ] [ reportMatrix true | false ] pairing-options Although, it seems I would have to do this manually 99 times for each pair of coordsets of the trajectory. Additionally, I am not sure I have the correct syntax for choosing a coordset from a model: align #1 , 1 toAtoms #1 ,2 gave me the following output: align #1 , 1 toAtoms #1 ,2RMSD between 8094 atom pairs is 0.000 angstroms That probably shouldn't be that accurate, right? In PyMOL one would use the command: intra_fit <model name> in order to do this. The best I was able to deduce was the following command: coordset #1 1,100 holdSteady @ca I am not sure if this is doing the same thing (rmsd fitting of model #1 coordset 1 to model #1 coordset 2.... ....model #1 coordset 99 to model #1 coordset 100 ) but rather just fixing the C-alpha atoms in place? is this equivalent? Also, I noticed this only aligns the coordsets once, and then reverts back to the default trajectory of tumbling around with all the rotations and translations. How can I set this holdSteady to be permanent for all future plays of my trajectory? Best, Yishai

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2D labels colored by chain color
by NG, Cheukhei Jackie [Student] 19 Aug '24

19 Aug '24

Dear sir/madam, I am trying to generate publication-quality images with chimeraX with appropriate 2D labels. 1. Is there a variable I could use to represent the coloring of my current chain so i can apply in the command where the selection is multiple chains: label sel color (the variable)? 2. is the an offset parameter or any relevant parameters in the 2D label command that are recommended for publication use? Thank you very much for your time. Thanks, Jackie [https://www.polyu.edu.hk/emaildisclaimer/PolyU_Email_Signature.jpg] Disclaimer: This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful. The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information.

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Feature of chimera
by Arpita Nandy 19 Aug '24

19 Aug '24

Hi, I am a PhD student from Germany and would like to make a figure where I can highlight specific proteins of interest in the mitoribosome complex of yeast. Could you please assist me to use ChimeraX in this context. Best regards Arpita Nandy

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Usage and Distribution of ChimeraX at our Upcoming Max Planck Institute Summer School
by SantaLucia, Daniel 15 Aug '24

15 Aug '24

Hello ChimeraX team, My name is Dan SantaLucia; I'm a research scientist working under Prof. Frank Neese and Prof. Serena DeBeer at the Max Planck Institute for Chemical Energy Conversion. One thing we do every year is to organize a summer school for students from all over the world, where they get to learn in-depth about many different spectroscopic techniques as well as quantum chemical calculations to help them in their interpretations of these datasets. You can find more information here, if you're curious: https://summerschool.cec.mpg.de/en/home thing that would be really nice would be to offer students the ability to use ChimeraX alongside our tutorial/practical sessions. We use ORCA to do calculations (considering, of course, that Frank invented it), and we've found that ChimeraX has a lot of really nice features that would be perfect for helping the students to learn. What I wanted to ask was this: do we have permission to distribute the download files at: https://www.rbvi.ucsf.edu/chimerax/download.html to the students? They would be distributed on flash drives that we give to the students, and we would distribute the Windows, Mac, and Linux versions so that we could cover all users. The internet connection is not the best, unfortunately, at our venue, which is why they can't just go to the link to download it themselves. To be clear: this is a non-commercial use event, where we simply have international students coming to attend the summer school, and this is an event that is for learning purposes only. Nonetheless, I want to have your explicit permission for distribution of ChimeraX to the students as well as your permission for them to use your software at our summer school? Thanks so much, and looking forward to hearing back from you, -Dan [1668779311055] [1668779979115] Dr. Daniel J. SantaLucia MPI-KoFo/CEC Joint Workspace Stiftstraße 34-36 45470 Mülheim an der Ruhr Germany Tel.: +49 208 306 3724

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problem to open a swiss dock results file
by Aurélie Hoeffel 13 Aug '24

13 Aug '24

Dear Chimeras members, I would be interested to use chimera x for interpreting some results of my docking. I precise it is the first time I use swiss dock as well as chimera x, after receiving the swiss dock file in a tar.gz format, I compress it via 7Zip but then chimera x, is not able to process and open my document, ii is just written, tar data ,Unrecognized file suffix '.tar', so I do not kwo if the pb come from chimera or swiss dock, do you know how I can solve the problem? Thanks in advance, Aurelie

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ChimeraX-daily (1.9, 5 Aug 2024); Log panel stealing focus
by leeyang+chimerax＠gmail.com 10 Aug '24

10 Aug '24

Hi, Downloaded the above Daily (macOS 14.5, Universal), primarily for the workaround retrieving mmCIFs containing an underscore (#15557). I noticed that the Log toolpanel steals focus whenever it updates. Perhaps something that has already been dealt with? Otherwise, thought I should post it here. Cheers, Yang

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AlphaFold version in ChimeraX 1.8
by Anna Mestre Borras 09 Aug '24

09 Aug '24

Hi, I would like to confirm which is the AlphaFold version in ChimeraX 1.8 when using Tools --> structure prediction --> AlphaFold. Thanks! Best, Anna

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Could not display the lipid such as cardiolipin
by 杨雪梅 08 Aug '24

08 Aug '24

Dear ChimeraX support group, When I open my PDB with ChimeraX, some lipids (get from the coot library with three-code) could not be seen. When it open with pymol, the lipids were displayed normal. Have you met such problem and how did you fix it? Looking forward to your kind help. Sincerely yours, Xuemei Yang Chinese Academy of Sciences Shanghai Institute of Materia Medica

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Could not display the lipid such as cardiolipin
by Yang Xuemei 08 Aug '24

08 Aug '24

Dear ChimeraX support group, When I open my PDB with ChimeraX, some lipids (get from the coot library with three-code) could not be seen. When it open with pymol, the lipids were displayed normal. Have you met such problem and how did you fix it? Looking forward to your kind help. Sincerely yours, Xuemei Yang Fudan University Chinese Academy of Sciences Shanghai Institute of Materia Medica

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problem for the PDB deposition
by Yanhe Zhao 07 Aug '24

07 Aug '24

Dear ChimeraX community and developer, I am trying to deposit my map with model. I save the model from pdb to cif in ChimeraX because of large amount of atoms, then got error as "Missing '_entity_poly.pdbx_strand_id' item. I tired to use pymol to open my pdb and save it as cif by 'Export Molecule', in which I just use the default options. I checked the saved cif in ChimeraX, which is weird since it couldn't be show in cartoon style. Is there any easy to handle this in ChimeraX or any option should be used in the 'Export Molecule' in Pymol? Thanks and cheers, Yanhe

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Inverted fit in map ?
by GOVAERTS Cédric 07 Aug '24

07 Aug '24

Hi Team I would like to compare to conformations of a protein whose structures have been solved by cryoEM (conf1 with map1 and conf2 with map2) So I want to have the coordinates *and* the cryoEM maps aligned. Aligning the two conformations is easy thanks to matchmaker (align conf1 to conf2) However, I can I align map2 onto conf2 so that I can compare with map1 ? Basically I would like to do an “inverse” fit into map conf2->map2. Can I do that ? Note : I do not want to align map2 ontomap1 because of resolution and structural differences, the superimposition should be done at the coordinate level (actually on a subset of it which is easy in matchmaker). Thanks ! Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77<tel:+3226505377> Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/

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Question regarding per-Residue RMSD
by Zimiao Meng 07 Aug '24

07 Aug '24

Dear Developers/Researchers of ChimeraX, I'm a student researcher trying to utilize ChimeraX to analyze structures of models predicted by programs. Currently, when I do matchmaker, only the RMSD value is displayed. I'd like to know the per-residue RMSD (which should also be the alignment error for that residue) for a section of the sequence that's a few hundred residues long. I wonder if there is a way to display the information that ChimeraX used to calculate the overall RMSD? Or would the only way to do it be writing a python script? Best, Zimiao

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Looking for scale
by David S. Fay 07 Aug '24

07 Aug '24

Hi, Does anyone know if a reference-type PAE bar exists for the ChimeraX PAE plot when using the Rainbow (orange/yellow/blue) selection? Something similar to what AF provides for the (green) scale (below) or the electro-charge (blue/white/red) maps? Rainbow provides a nice visual range, but I couldn't find an associated score reference. [cid:7001d3eb-43d0-4009-9596-6843ea44695a@namprd05.prod.outlook.com] Thanks, David

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ChimeraX website not accessible from time to time
by Roden Deng Luo 07 Aug '24

07 Aug '24

Hi, This has happened quite some times in the last few months. I realized just now that I could not access https://www.cgl.ucsf.edu/chimerax/docs/devel/modules/core/logger.html. I then checked the following, and all were not working. Is this my own problem or a server-side issue? Is there an offline developer documentation (PDF or HTML)? https://www.cgl.ucsf.edu/chimerax/docs/user/commands/log.html https://www.cgl.ucsf.edu/chimerax/download.html https://www.cgl.ucsf.edu/chimerax/docs/licensing.html Many thanks, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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PhenixUI Installation Errors
by Caballero Silva, Guillermo 06 Aug '24

06 Aug '24

Good afternoon, I am a current postdoctoral fellow working primarily with low resolution (4-6A) CryoEM Data/Models and recently discovered the "Local EM Fitting Tool" described in https://doi.org/10.1101/2024.05.16.594509 which I believe will help me overcome some of the issues I am currently experiencing in model docking/building. I am currently running ChimeraX version 1.5 and Phenix-1.20.1-4487 and have been trying to install PhenixUI from ChimeraX "More Tools" but have not been able to. I have tried installing older version of PhenixUI but was only able to install PhenixUI version 1.0.5. When I try to upgrade to the current version I am received with the following message: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\gcaballe\downloads\chimerax_phenixui-1.2.2-py3-none-any.whl Requirement already satisfied: ChimeraX-MapData~=2.0 in c:\users\gcaballe\documents\chimerax\bin\lib\site-packages (from ChimeraX-PhenixUI==1.2.2) (2.0) ERROR: Could not find a version that satisfies the requirement ChimeraX-Map~=1.1.3 (from chimerax-phenixui) (from versions: none) ERROR: No matching distribution found for ChimeraX-Map~=1.1.3 [notice] A new release of pip available: 22.2.2 -> 24.2 [notice] To update, run: C:\Users\gcaballe\Documents\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip It is my understanding that I need to install "ChimeraX-Map~=1.1.3" but cannot find how/where to do so. My current OS is Windows x64. Is it possible to install Local EM Fitting with my current set up or do I need to do any changes modifications. Please let me know if there is any more information I can provide and thank you in advance for your help and support. Kind regards, Guillermo Caballero Silva Postdoctoral Fellow Amgen Canada [cid:image001.png@01DAE4FC.105C31E0]

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Doubt about "contacts" command in ChimeraX
by Manuel Ospina 05 Aug '24

05 Aug '24

Good evening, I am actually using ChimeraX and I am trying to figure out a command that can show me all the contacts of my ligand below 3.0A with my protein. Unfortunately, I have not found anything clear enough to do so. Is there a way to do this? Another doubt is, if I have labelled 2 contacts (i.e 2.576A and 3.149A) but I am interested in only showing the label " 2.576A", I try deleting the other contact label (" 3.149A") by selecting it and typing the "label del" command, but this will delete my label of interest as well. Is there a way of only deleting specific labels from the contacts? Any help is appreciated. Best regards, Manuel

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Silhoutte
by Shubhangi Agarwal 05 Aug '24

05 Aug '24

Dear developers, I am trying to outline surfacerepresentation of my protein structure with the silhouette feature but it gives me black dashes along rest of the surface which I don’t want, how can I just use the black borderline feature for my surface and protein? Figure attached below. Thank you Shubhangi [cid:922B93FD-C686-4CED-8281-EFF2FAFC08D2]

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2D PAE plot with colored PAE domains
by David S. Fay 05 Aug '24

05 Aug '24

Hi All, Was trying to get the ChimeraX 2D PAE plot to display the colored PAE domains consistent with the ribbon diagram. The button “Color PAE Domains” colors the ribbon diagram by coherent domains, but the 2D plot is still colored by PAE (error). The Meng et al., 2023 has nice examples of this (e.g., 1f) coloring. Thanks in advance! David

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save images
by Aritz Roa Eguiara 02 Aug '24

02 Aug '24

Dear Sir or Madam, I am trying to make a default .cxc file that I can use to automatically save the view for publication. I am using the following: save /path/image.tiff pixelSize 0.05 supersample 4 This turned out to give me the best files for most cases, but depending on the zoom I get different file sizes. Is there any way to have a standard command that gives me high quality images and that always have the same dimensions regardless of the zoom? I understand that the issue comes from the different pixel size of the zoom and that I am specifying a pixel size on the command, but when trying other alternatives I have not been successful to get proper images... All the best, Aritz

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August 1 Chimera(X) website downtime
by Elaine Meng 01 Aug '24

01 Aug '24

Planned downtime for server maintenance: The Chimera and ChimeraX websites, Toolshed, web services (Blast Protein, Modeller, ...) and cgl.ucsf.edu e-mail will be unavailable August 1, 3-6 pm PDT. Apologies for any inconvenience, 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

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