- ChimeraX-users - RBVI Mailing Lists

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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