- ChimeraX-users - RBVI Mailing Lists

ChimeraX with Modeller
by Matt Goff 10 Dec '24

10 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 06 Dec '24

06 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 04 Dec '24

04 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/ >>

1 0

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

3 10

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

4 14

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

2 2

Question about using AF3-competitor outputs
by David S. Fay 27 Nov '24

27 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

3 4

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

2 1

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  

2 1

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.

2 2

ChimeraX opening failure
by gianmarco.elisi＠gmail.com 26 Nov '24

26 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 26 Nov '24

26 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 07 Nov '24

07 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 07 Nov '24

07 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

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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

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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 06 Nov '24

06 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.

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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

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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 02 Nov '24

02 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

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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

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