- ChimeraX-users - RBVI Mailing Lists

How to activate the Extract button in Segment Map function?
by Bo Chen 25 Sep '23

25 Sep '23

Dear ChimeraX, I tried to use Segment Map to remove some portions of the cryoEM map, and extract the selected portion, but the extract button remains shaded. The only tab in the "other tools" row that appears to be activated is "Fit". I have the most recent version of ChimeraX installaed(Sept 19). Could you give me some hints how to activate the extract in "Other tools" under the "Shortcut options" in "Segment Map"? Thanks! Bo

3 2

Changing mesh size to save as STL file
by Arthur Melo 25 Sep '23

25 Sep '23

Dear colleagues, Is there a way to refine or decimate a mesh of a map to save as an STL file? All the best, Arthur

2 2

symmetrizing the model
by Dmitry Semchonok 22 Sep '23

22 Sep '23

Dear colleagues, A very quick question - what is the command to apply the symmetry to the 3D model? (please provide a usage example if possible). Will the soft generate the symmetrized model after this command application? I found the one for Chimera but not for ChimeraX. Many thanks. Sincerely, Dmitry

3 4

Equivalents to sop split & mask?
by Oliver Clarke 21 Sep '23

21 Sep '23

Hi, Is there a direct equivalent to the command “sop split” in ChimeraX? In the documentation for the “surface” command, I can see that there is an option to split by color, but not to split into individually selectable blobs. We use this a lot in Chimera, as a quick way to make a starting point for a mask to use in refinement, so it would be great to have in ChimeraX too. Also, is there an equivalent to the “mask” command from Chimera? I can’t seem to find it but perhaps it has a different name? Cheers Oli

3 3

Labels of selected residues even with their model name
by svle＠tiscali.it 21 Sep '23

21 Sep '23

Hi, I have used matchmaker with four loaded models to compare the side chains orientation of some selected residues. It is possible to label the selected residues even with the information of the model name they belong to? Thanks. Saverio

3 3

Open and play volume series in ChimeraX
by Wout Oosterheert 20 Sep '23

20 Sep '23

Dear ChimeraX team, I’m currently trying to open a volume and play a volume series in ChimeraX. According to the website (https://www.cgl.ucsf.edu/chimerax/docs/user/trajectories.html) opening a volume series should work like this: “Volume data can be opened as a series with open, employing filename wildcard symbols or globbing as needed to specify multiple files in a single command”. This seems simple enough, I indeed can open the volumes as a group. However, when I then try to play the series using: vseries play #1 direction oscillate loop true, I get the error: no volume series specified. Could you explain to me how I can get my group of volumes recognized as a volume series? The vseries page (https://www.cgl.ucsf.edu/chimerax/docs/user/commands/vseries.html) is very elaborate, but I cannot find alternative options of opening my volumes as a series. I know how to do things in regular Chimera, but would prefer to stick with ChimeraX because I make all my other figures with it. Thank you very much in advance!! Best, Wout Wout Oosterheert, PhD Humboldt Postdoctoral Fellow Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund, Germany Phone +49-(0)231-133-2357 Email: wout.oosterheert(a)mpi-dortmund.mpg.de<mailto:wout.oosterheert@mpi-dortmund.mpg.de>

2 2

seq_rmsd and align command
by dng26＠mrc-mbu.cam.ac.uk 19 Sep '23

19 Sep '23

Hello, I have two PDB models I am comparing, but I am having some issues generating the seq_rmsd attribute across all of the chains in the superposition that I want. My current models (same protein, but different states and slightly altered built sequences) have chains A/B/C/D/E/F separated over two domains of A/B/C and D/E/F, for example. My problem is that domain D/E/F is much larger than the former and when I run a matchmaker command such as this: matchmaker #1/A/B/C/D/E/F to #2/A/B/C/D/E/F pairing ss show true I get the resulting superposition favoring the /D/E/F domain (larger RMSD values on A/B/C). This would be fine, however, I want to investigate RMSD variation in D/E/F relative to a fixed position of A/B/C. If I run the following command I only get pairwise RMSDs (seq_rmsd header) for the specified chains but lack those of the larger D/E/F domain as they are not included. matchmaker #1/A/B/C to #2/A/B/C pairing ss show true I look to Calculate the RMSD between paired residues of chains /A/B/C/D/E/F without moving the current structures (after ‘mmaker’ alignment to A/B/C) with the ‘align’ command but the ‘move’ option set to nothing: align #1/A/B/C/D/E/F toAtoms #2/A/B/C/D/E/F move nothing matchNumbering (or matchAtomNames also tested) true I believe the above is what I want with regards to superposition for the RMSD calculations, but the ‘align’ job does not appear to give a seq_rmsd header attribute once run, even though the log seems to suggest it does a pairwise residue alignment to calculate the RMSDs. (Possibly because it does not just look at the CA like matchmaker does?) Is there a way to generate seq_rmsd attributes from the ‘align’ command, or is there a way to have an equivalent ‘move nothing’ in ‘mmaker’? I am looking to use seq_rmsd information to color the model and I am using v1.6.1. Any help is much appreciated! Dan.

2 2

Chimerax
by François Ferron 15 Sep '23

15 Sep '23

Hi I am making a figure using a pdb and a density map in chimeraX1.6.1. each time I do that I have coloured arrows representing an axis that is in the middle. how do I get rid of them. I am sure it is trivial but I just could not find the answers in the manual. thanks François -- François Ferron, Ph.D. francois.ferron(a)univ-amu.fr @F2erron@fediscience.org Laboratoire CNRS - UMR 7257 (AFMB) AFMB - POLYTECH Case 925 163, Av de Luminy 13288 Marseille Cedex 09 France & European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany ######################################### Success is not final, failure is not fatal; it's the courage to continue that counts.

2 2

Request to Resolve the Issue of Modifying Surface Dot Size in ChimeraX
by 18802001045＠163.com 14 Sep '23

14 Sep '23

Dear ChimeraX Maintenance Team, I hope this email finds you well. I am writing to seek assistance regarding an issue I have encountered while working with protein models in ChimeraX. After performing MPL calculations on protein models, I have found that I am unable to modify the dot size of the resulting surface representation. In Chimera, this task was easily accomplished through the "Model Panel" by adjusting the "MSMS Model Attributes". However, I have not been able to find a similar option or command in ChimeraX. I would greatly appreciate it if you could provide guidance or suggest a solution to address this matter. Being able to adjust the dot size of the surface representation is crucial for my current research project, and I rely heavily on the functionalities provided by ChimeraX. Thank you very much for your attention to this matter. I look forward to your kind assistance and prompt response. Best regards, Zhuangwei Zhang, Ph.D. State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Centre of Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University E-mail: dg21240166(a)smail.nju.edu.cn

5 4

Monitor distance angle and torsion angles along trajectoty
by CUNIASSE Philippe 14 Sep '23

14 Sep '23

Dear all, I am wondering if there is a mean in ChimeraX to monitor distances, angles and torsion angles along a MD trajectory. The ideal would be to export a vector containing the frame id (a number) and the value measured for the distance or torsion angle. At the moment I can only built a distance histogram (which is already very usefull) after having created a pseudobond. But doing this, you lose the time evolution along the trajectory. Thanks in advance for your help. Best regards. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:philippe.cuniasse@cea.fr> Web: http://biodev.cea.fr/rasmot3d/ [signature_575242473][signature_2653780937][signature_3407707164] -----------------------------------------------

2 2

Setting default volume step and rms level
by Samuel Haysom 13 Sep '23

13 Sep '23

Hello, Is it possible to change the default step and level that ChimeraX uses when it opens maps? My data (cryoEM) mostly opens at step 2 with the level set too low for useful viewing, necessitating adjusting these settings for every map I open. Is there a global setting that I can change (for instance by specifying it in a startup script) to change this behaviour so my maps always open at step 1 and at a specified level (say rmsLevel 8)? KR, Sam Samuel Haysom | Research Scientist | Biophysics Sosei Heptares | T: +44 (0)1223 949201 Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, United Kingdom The information in this e-mail is confidential and may be legally privileged. It is intended for the exclusive attention of the addressee stated above and should not be copied or disclosed to any other. If you have received this transmission in error, please contact the sender immediately, make no use of its contents and delete this message from your system. Contact and registered office address: Heptares Therapeutics Limited, Granta Park, Great Abington, Cambridge, CB21 6DG. Company No: 06267989.

4 5

Advice on handling cofactor-protein electrostatic interactions
by Boaz Shaanan 12 Sep '23

12 Sep '23

Hi, I would like to present effects of mutations around cofactors (TDP derivatives) on the protein - cofactors electrostatic interactions. I use APBS and chimerax to display the electrostatic surface potential of the protein, but since PDB2PQR eliminates the cofactor from the pqr file I need a tool for the cofactor surface potential. I'm wondering what tool I should use for this. Is it Antechamber+chimerax or something else? Is there by chance a demo for such scenario? I'd appreciate your advice. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Fax: 972-8-647-2992 or 972-8-646-1710

2 7

ChimeraX "Fly" Command
by Kayla Deuter 12 Sep '23

12 Sep '23

Good afternoon, I am emailing you to try and troubleshoot the ChimeraX software I am currently using. I just recently downloaded ChimeraX 1.1.1 and I am operating on a Macbook Pro with High Sierra 10.13.6 software. I am currently teaching myself the program by watching tutorials and referencing the User Guide. Everything seems to work fine except for the "fly" command. I am trying to record movies for practice and examples but every command works except for the "fly" command. I went into the user guide, I've tried researching the issue, and I've done about all I can do to try resolving this issue on my own. After I create my view points, I attempt to create transitions by typing "fly view 1 view 2" but every time I try typing fly it always says command unknown and gives me error messages. When I try to further investigate the error code, it is useless and I get no answers. If there is anything I can do to fix this, please let me know. The fly command is crucial for creating a smooth animation. Best, Kayla Deuter

2 1

Re: Trouble installing plugin
by Eric Pettersen 12 Sep '23

12 Sep '23

Hi Barry, We continue to work on this issue, but have not yet succeeded in getting installation as a source dependency to work. We hope to get it resolved soon, but it's hard to say exactly how long it will take, so in the interest of allowing you to make progress I suggest using an alternate approach -- include mdtraj as an additional package in your bundle. In your bundle_info.xml you would use an AdditionalPackages tag with a child tag of "Package" which has a "name" attribute of "mdtraj" and a "folder" attribute of wherever mdtraj got installed. Since mdtraj is not pure Python, you would also have to use a "platform" attribute of mac/linux/windows. If you also built mdtraj on other platforms you could copy it over to the machine you're building the bundle on and include additional Package tags with different platform/folder values. You also have to have a DataFiles tag with a "package" attribute of "mdtraj" and an appropriate "platform" attribute, with child DataDir/DataFile tags enumerating what to copy from the installation. One thing to keep in mind is that the installation has to be compatible with the version of Python ChimeraX is using, which is Python 3.9 for ChimeraX 1.6.1 and Python 3.11 for the daily build. So you would want to include the corresponding dependency on ChimeraX-Core. Also, a binary version of mdtraj is available for Mac (Python 3.9) so you could conceivably include that directly as a dependency (i.e. in a Dependency tag rather than a Package tag) with a "mac" platform attribute and a ChimeraX-Core dependency of ==1.6.1. For reference, SEQCROW uses the AdditionalPackages tag in its bundle_info.xml, which you can see here. <https://github.com/QChASM/SEQCROW/blob/master/bundle_info.xml> --Eric Eric Pettersen UCSF Computer Graphics Lab > OK. So, we decided to wipe some computers and start fresh to install our plugin. And using the daily build from a couple days ago and a daily build from 7-15 and always on a freshly built linux 20.04 system we are unable to install my plugin. However, it somehow installed in the past on my coworker's system (using 7-15 chimerax) and my system (using 6-6 chimerax). He and I can both repeatedly install and uninstall my plugin. But any clean system will not "devel install" the plugin. Below is the latest log output using the daily build from 7-15 (because we have one user successfully using it). I am at a real loss as to what is going on. FWIW the clean systems do also have python 2.7. I know recently you fixed a problem of installing a plugin on a system that has python 2.7 on it. Please let me know what I can do. Our plugin is alpha ready and if I can't get it easily installable then our project is at a standstill.

1 1

Lock model(s) to rotation/translation?
by Oliver Clarke 08 Sep '23

08 Sep '23

Hi, I know that in ChimeraX the preferred way to manipulate models with respect to one another is using the mouse modes. This works, but is still (in my experience) less precise/ergonomic than deactivating selected models in Chimera and freely manipulating the remaining active models using the trackpad/mouse. Is there any possibility in the future (or present) of adding the capacity to “lock" selected models to rotation/translation, to allow free manipulation of the remainder? Cheers Oli

2 14

Add model number to pop up balloon?
by Oliver Clarke 08 Sep '23

08 Sep '23

Hi, Currently the info in the pop up balloon that appears when one hovers over a residue is of the following format: res-name res-num.chain atom-name. Would it be possible to add the model number at the start? The model number is in the pop up balloon for maps, but not atomic models, and it would be convenient to have it to avoid having to bring up the model panel when typing commands. Cheers Oli

2 2

Re: Trouble installing plugin
by Zach Pearson 08 Sep '23

08 Sep '23

Per https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/8927 which broke on the same dependency (mdtraj), dealing with recursive pip was such a nightmare that ChimeraX’s pip command searches for the python executable _next to_ ChimeraX.exe and uses that instead of ChimeraX; toolshed_utils will have to do the same to fix this error. — Zach > On Aug 30, 2023, at 14:40, Tom Goddard <goddard(a)sonic.net> wrote: > > Hopefully Zach or Greg can help you with this pip install error. > > Tom > > >> On Aug 30, 2023, at 2:19 PM, BARRY E DEZONIA via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> OK, so we have now installed chimerax-daily on another system that already had it on there. We were getting similar errors as detailed in my earlier email. After carefully cleaning the system and removing and reinstalling the July 14 daily build we are still getting install errors for my plugin. Instead of the python 3.9 complaints they are now python3.11 complaints. So that part of the earlier problem was fixed by my cleanups. But it is still broken. We still have pip running problems. Even with upgrading chimerax's python's pip and making sure that the chimerax's pip's bin dir is in the path. The error message is basically "AssertionError: Cannot run __pip-runner__.py as a non-main module". I will post the (lengthy) log output of my plugin install process below. Please let us know what might be causing this. We were just going to install a new daily build but your website has been down today. >> >> ==================================================== >> >> UCSF ChimeraX version: 1.7.dev202307150241 (2023-07-15) >> © 2016-2023 Regents of the University of California. All rights reserved. >> How to cite UCSF ChimeraX >> devel install /home/crow/bphon/bphon/chimerax-plugin/tut_tool_qtrunning build >> running build_py >> running bdist_wheel >> installing to build/bdist.linux-x86_64/wheel >> running install >> running install_lib >> creating build/bdist.linux-x86_64/wheel >> creating build/bdist.linux-x86_64/wheel/chimerax >> creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt >> copying build/lib/chimerax/tut_tool_qt/tool.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt >> copying build/lib/chimerax/tut_tool_qt/__init__.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt >> creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable >> copying build/lib/chimerax/tut_tool_qt/Runnable/zncc.sh -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable >> copying build/lib/chimerax/tut_tool_qt/Runnable/zncc.jar -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable >> copying build/lib/chimerax/tut_tool_qt/Runnable/simCC.com <http://simcc.com/> -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable >> copying build/lib/chimerax/tut_tool_qt/Runnable/simNC.com <http://simnc.com/> -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Runnable >> creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable >> copying build/lib/chimerax/tut_tool_qt/Installable/install_traj2nmr.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable >> creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/README.md -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/setup.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr >> creating build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/session.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/ucsf.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/__init__.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/resonance.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/shifts.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/utils.py -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr >> copying build/lib/chimerax/tut_tool_qt/Installable/traj2nmr/LICENSE -> build/bdist.linux-x86_64/wheel/chimerax/tut_tool_qt/Installable/traj2nmr >> running install_egg_info >> running egg_info >> writing ChimeraX_BphonTool.egg-info/PKG-INFO >> writing dependency_links to ChimeraX_BphonTool.egg-info/dependency_links.txt >> writing requirements to ChimeraX_BphonTool.egg-info/requires.txt >> writing top-level names to ChimeraX_BphonTool.egg-info/top_level.txt >> reading manifest file 'ChimeraX_BphonTool.egg-info/SOURCES.txt' >> writing manifest file 'ChimeraX_BphonTool.egg-info/SOURCES.txt' >> Copying ChimeraX_BphonTool.egg-info to build/bdist.linux-x86_64/wheel/ChimeraX_BphonTool-0.4-py3.11.egg-info >> running install_scripts >> creating build/bdist.linux-x86_64/wheel/ChimeraX_BphonTool-0.4.dist-info/WHEEL >> creating 'dist/ChimeraX_BphonTool-0.4-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it >> adding 'chimerax/tut_tool_qt/__init__.py' >> adding 'chimerax/tut_tool_qt/tool.py' >> adding 'chimerax/tut_tool_qt/Installable/install_traj2nmr.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/LICENSE' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/README.md' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/setup.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/__init__.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/resonance.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/session.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/shifts.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/ucsf.py' >> adding 'chimerax/tut_tool_qt/Installable/traj2nmr/traj2nmr/utils.py' >> adding 'chimerax/tut_tool_qt/Runnable/simCC.com <http://simcc.com/>' >> adding 'chimerax/tut_tool_qt/Runnable/simNC.com <http://simnc.com/>' >> adding 'chimerax/tut_tool_qt/Runnable/zncc.jar' >> adding 'chimerax/tut_tool_qt/Runnable/zncc.sh' >> adding 'ChimeraX_BphonTool-0.4.dist-info/METADATA' >> adding 'ChimeraX_BphonTool-0.4.dist-info/WHEEL' >> adding 'ChimeraX_BphonTool-0.4.dist-info/top_level.txt' >> adding 'ChimeraX_BphonTool-0.4.dist-info/RECORD' >> removing build/bdist.linux-x86_64/wheel >> Distribution is in /home/crow/bphon/bphon/chimerax-plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl >> [toolshed install](help:user/commands/toolshed.html#install) >> /home/crow/bphon/bphon/chimerax- >> plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl >> >> [toolshed install /home/crow/bphon/bphon/chimerax- >> plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none- >> any.whl](cxcmd:toolshed install /home/crow/bphon/bphon/chimerax- >> plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl) >> >> Traceback (most recent call last): >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 517, in _pip_install >> results = _run_logged_pip(command, logger) >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 583, in _run_logged_pip >> raise RuntimeError(s) >> RuntimeError: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ >> Processing /home/crow/bphon/bphon/chimerax-plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl >> Requirement already satisfied: ChimeraX-Core~=1.1 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-BphonTool==0.4) (1.7.dev202307150241) >> Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-BphonTool==0.4) (1.30.2) >> Collecting mdtraj (from ChimeraX-BphonTool==0.4) >> Using cached mdtraj-1.9.9.tar.gz (2.2 MB) >> Installing build dependencies: started >> Installing build dependencies: finished with status 'error' >> error: subprocess-exited-with-error >> >> × pip subprocess to install build dependencies did not run successfully. >> │ exit code: 1 >> ╰─> [22 lines of output] >> ERROR: >> Traceback (most recent call last): >> File "<frozen runpy>", line 198, in _run_module_as_main >> File "<frozen runpy>", line 88, in _run_code >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- >> packages/chimerax/core/__main__.py", line 1044, in <module> >> exit_code = init(sys.argv) >> ^^^^^^^^^^^^^^ >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- >> packages/chimerax/core/__main__.py", line 801, in init >> runpy.run_path(opts.run_path) >> File "<frozen runpy>", line 291, in run_path >> File "<frozen runpy>", line 98, in _run_module_code >> File "<frozen runpy>", line 88, in _run_code >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/pip/__pip- >> runner__.py", line 49, in <module> >> assert __name__ == "__main__", "Cannot run __pip-runner__.py as a non-main >> module" >> ^^^^^^^^^^^^^^^^^^^^^^ >> AssertionError: Cannot run __pip-runner__.py as a non-main module >> >> >> [end of output] >> >> note: This error originates from a subprocess, and is likely not a problem with pip. >> error: subprocess-exited-with-error >> >> × pip subprocess to install build dependencies did not run successfully. >> │ exit code: 1 >> ╰─> See above for output. >> >> note: This error originates from a subprocess, and is likely not a problem with pip. >> >> >> During handling of the above exception, another exception occurred: >> >> Traceback (most recent call last): >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/devel.py", line 174, in _run >> unbound_method(bb, *args, **kw) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/bundle_builder/bundle_builder.py", line 154, in make_install >> run(session, cmd) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 38, in run >> results = command.run(text, log=log, return_json=return_json) >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2897, in run >> result = ci.function(session, **kw_args) >> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/toolshed.py", line 301, in toolshed_install >> ts.install_bundle(bundles, logger, **kw) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 916, in install_bundle >> _install_bundle(self, bundle, logger, per_user=per_user, reinstall=reinstall, session=session, no_deps=no_deps) >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 252, in _install_bundle >> results = _pip_install( >> ^^^^^^^^^^^^^ >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/toolshed_utils/__init__.py", line 520, in _pip_install >> raise UserError(str(e)) >> chimerax.core.errors.UserError: Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ >> Processing /home/crow/bphon/bphon/chimerax-plugin/tut_tool_qt/dist/ChimeraX_BphonTool-0.4-py3-none-any.whl >> Requirement already satisfied: ChimeraX-Core~=1.1 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-BphonTool==0.4) (1.7.dev202307150241) >> Requirement already satisfied: ChimeraX-UI~=1.0 in /usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages (from ChimeraX-BphonTool==0.4) (1.30.2) >> Collecting mdtraj (from ChimeraX-BphonTool==0.4) >> Using cached mdtraj-1.9.9.tar.gz (2.2 MB) >> Installing build dependencies: started >> Installing build dependencies: finished with status 'error' >> error: subprocess-exited-with-error >> >> × pip subprocess to install build dependencies did not run successfully. >> │ exit code: 1 >> ╰─> [22 lines of output] >> ERROR: >> Traceback (most recent call last): >> File "<frozen runpy>", line 198, in _run_module_as_main >> File "<frozen runpy>", line 88, in _run_code >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- >> packages/chimerax/core/__main__.py", line 1044, in <module> >> exit_code = init(sys.argv) >> ^^^^^^^^^^^^^^ >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site- >> packages/chimerax/core/__main__.py", line 801, in init >> runpy.run_path(opts.run_path) >> File "<frozen runpy>", line 291, in run_path >> File "<frozen runpy>", line 98, in _run_module_code >> File "<frozen runpy>", line 88, in _run_code >> File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/pip/__pip- >> runner__.py", line 49, in <module> >> assert __name__ == "__main__", "Cannot run __pip-runner__.py as a non-main >> module" >> ^^^^^^^^^^^^^^^^^^^^^^ >> AssertionError: Cannot run __pip-runner__.py as a non-main module >> >> >> [end of output] >> >> note: This error originates from a subprocess, and is likely not a problem with pip. >> error: subprocess-exited-with-error >> >> × pip subprocess to install build dependencies did not run successfully. >> │ exit code: 1 >> ╰─> See above for output. >> >> note: This error originates from a subprocess, and is likely not a problem with pip. >> >> From: Tom Goddard <goddard(a)sonic.net> >> Sent: Thursday, August 24, 2023 9:49 PM >> To: BARRY E DEZONIA <barry.dezonia(a)wisc.edu> >> Cc: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> >> Subject: Re: [chimerax-users] Trouble installing plugin >> >> The ChimeraX daily build is using Python 3.11 and your error message includes paths to Python 3.9. It will probably cause havoc if you have both in your same ChimeraX installation. >> >> ChimeraX developers Greg or Zach who know more about Linux would have to comment on whether it is even possible to install ChimeraX over another ChimeraX without the original copy being deleted. And they also work on the "devel install" command. >> >> Tom >> >> >>> On Aug 24, 2023, at 12:08 PM, BARRY E DEZONIA via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> It is possible that on my home machine I installed the latest daily build over an earlier daily build. >>> From: BARRY E DEZONIA via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> >>> Sent: Thursday, August 24, 2023 6:33 AM >>> To: chimerax-users(a)cgl.ucsf.edu <chimerax-users(a)cgl.ucsf.edu> >>> Subject: [chimerax-users] Trouble installing plugin >>> >>> I am having trouble installing a plugin I am developing. It works on one system I am using at work and fails on my system at home. The home system has the latest daily build on it. The work system has an earlier daily build on it. >>> >>> This is what I try to do inside chimerax: >>> >>> devel install ~/dev/bphon/chimerax-plugin/tut_tool_qt >>> >>> And this is the installation error: >>> >>> open /usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/pip/__pip-runner__.pyTraceback (most recent call last): >>> File "/usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/pip/__pip-runner__.py", line 49, in <module> >>> assert __name__ == "__main__", "Cannot run __pip-runner__.py as a non-main module" >>> AssertionError: Cannot run __pip-runner__.py as a non-main module >>> >>> Error opening python file /usr/lib/ucsf-chimerax-daily/lib/python3.9/site-packages/pip/__pip-runner__.py >>> >>> Any idea what is happening? I may have run into this problem some time ago on the work computer and fixed it but I honestly don't know. >>> >>> Please forward this to the bugs email list of it should go there instead. Thanks. >>> >>> Sorry for yet another question. You guy seems very busy with mail recently. >>> _______________________________________________ >>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >> >> _______________________________________________ >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >

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Coloring of trajectory using mpl command
by Alexander Hung Lee 08 Sep '23

08 Sep '23

Hello everyone, I'm sorry for bothering all of you so often these past few days... but I ran into another issue. I opened a pdb and corresponding trajectory .nc file, and I ran "mlp #1 key true". Lipophilicity coloring showed up, but when I played the trajectory, the mpl colors went away and the default colors came back. I noticed the same happened for "coulombic" command. For now, I'm making due with a custom attribute file and "color byattribute name palette lipophilicity" from this tutorial https://www.cgl.ucsf.edu/chimerax/docs/user/formats/defattr.html#examples. It does stay throughout the trajectory but doesn't look as good, and the colors aren't blended. I have also tried doing "mlp map true" and "color sample #1 map #2" with #1 being the pdb with trajectory and #2 the resulting map from mlp. It looked really bad. The protein is now one color. "mlp map true" command [cid:41c39c60-61c8-47ff-b996-f063b013d319] [cid:d2f10dad-4f81-40e6-99cc-407b2d96a17f] [cid:ec390e08-8756-45ce-af0d-8e8a03992457] Alex

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Selection syntax for atomic models vs surfaces/volumes?
by Oliver Clarke 06 Sep '23

06 Sep '23

Hi, Is there anything in the ChimeraX selection syntax to select by model type? For example, I would like to select only atomic models, excluding surfaces and volumes, and do something to them in a script or an alias - is there an efficient way of doing that? Right now, I can do this using "sel @*”, which selects everything is an atom, but I have the feeling that this is not so efficient (it is quite slow for large models). Cheers Oli

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inquiry
by Talha Shafi 06 Sep '23

06 Sep '23

hi I am using chimerax for model visualization. i wanted to inquire how can drag and rotate a selected model to manually overlap with my density may. in chimera1.13 version in model panel i could just uncheck the action option and perform my task. i can not figure this in chimerax to move my model over the density. fit in map is not able to align the models. may be manually aligning them and then perform fit to map works better. looking forward to hearing from you talha -- Talha Shafi Postdoc Scholar York Structure Biology Laboratory. University of York United Kingdom

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Dealing with artefact bonds
by Enrico Martinez 06 Sep '23

06 Sep '23

Dear Chimera-X users ! I am performing visualisation of the protein-protein complex obtained from md trajectory. The issue is that the pbd lacks the TER record between two different chains so Chimera-X recognises it as a bound complex and consequently adds a long unusual bond (>30A) between C term of one unit and N term on the another. Are there any commands that could be useful to omit such an artifact (e.g. to hide all bounds > 5 A etc) ? I found only a solution to hide several residues from the both units that will remove the long bond automatically. Many thanks in advance Enrico

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Aligning residue/ligand to foreground
by Alexander Hung Lee 05 Sep '23

05 Sep '23

Hello everyone, In old Chimera, I was able to center the ligand to the foreground of view using "align ligand ~ligand" no matter the orientation, if the ligand is in view or not. Is there a comparable way in ChimeraX? The same command gives "expected a keyword" and using "view ligand" or "view sel-residues zalign sel" does not bring it to foreground if it's behind something else. Thanks, Alex

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Predict a large protein structure with Alphafold2 and Chimerax
by Sara Qubisi 05 Sep '23

05 Sep '23

Hello Chimerax team. I am a postdoc at SICKKIDS hospital, and I am currently working on a project that involves large protein (~5400 aa). I am new to Alphafold and Chimerax and I want to perform a structure comparison between the wild type protein and a set of frameshift mutation (result in protein truncation) versions of the protein. I learned online and from your YouTube videos that I cannot enter more than 1200aa per assay request. Is there a way to overcome this where I can use the full protein sequence. Regards, Sara Qubisi. ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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[AMBER] Converted PSF file (prmtop > psf) failed to open in ChimeraX but did in old Chimera
by Alexander Hung Lee 05 Sep '23

05 Sep '23

Hello, I converted prmtop to psf to use with ChimeraX by just editing the suffix as suggested http://archive.ambermd.org/201902/0118.html and also converted it a second way with ParmEd. ChimeraX couldn't read either version and gave me the error "list index is out of range." I successfully opened the original prmtop and the two psf versions in the old Chimera with trajectory .nc file. What do I need to do? Alex

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save "side view" settings
by vincent Chaptal 05 Sep '23

05 Sep '23

Hi, I opened the side view dialog window and adjusted the view planes for a nice figure. I would like to save the parameters so I can go back and modify the figure at a later stage, but the setting are not stored in the "view matrix" command. Could you tell me which command can save these settings? (I'm using chimeraX 1.5). Thank you. Best Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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