October 2024 - ChimeraX-users - RBVI Mailing Lists

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

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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

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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

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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

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Installing ChimeraX in a Apptainer container
by tluchko 21 Oct '24

21 Oct '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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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.

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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

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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. >> >

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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

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