August 2023 - ChimeraX-users - RBVI Mailing Lists

Show side chain, main chain, and cartoon at the same time
by Zhang, Miao 22 Apr '24

22 Apr '24

Dear colleagues I am new to ChimeraX. I am trying to figure out how to show side chain, main chain, and cartoon at the same time in a protein structure. Like the one below made in other software. Could you please help? [cid:image001.png@01D9D154.CE3D4440] Best, - - - - - - - - - - - - - - - - - Miao Zhang Ph.D. Associate Professor Chapman University School of Pharmacy 9401 Jeronimo Rd, Suite 297W Irvine, CA 92618 Phone: 714-516-5478 http://www.chapman.edu/our-faculty/miao-zhang

2 18

Missing Vina on ChimeraX
by Luigi Marongiu 03 Apr '24

03 Apr '24

Dear sir or madam, I am using UCSF ChimeraX version 1.5 (2022-11-24). I have been trying to use AutoDock Vina but there is no such command in my version. How do I install it into ChimeraX (as shown in many tutorials, Vina is part of Chimera)? Thank you. Best regards, Luigi Marongiu Ph.D., B.Sc. (Hons.)

4 6

Colouring clipping plane
by GOVAERTS Cédric 20 Jan '24

20 Jan '24

Hi ChimeraX team. I’m trying to get an image of a protein whose surface is colored by electrostatic properties but clipped halfway. I would like the clipping plane to be white, not red/blue according to the electrostativ properties of the residues insides the protein. However, I don’t’ seem to be able to do that. -If I color everything white and then click on Molecular-Display “electrostatic”, the clipping plane also gets the electrostatic coloring [Graphical user interface Description automatically generated] -If I color everything white and then click on Molecular-Display “hydrophobic” or “rainbow” it works, the clipping plane remains white. [cid:image002.png@01D94092.6E8A2390] Can you help me getting the white clipping plane with electrostatic surface ? Thanks a bunch Cedric — Prof. Cedric Govaerts, Ph.D. Universite Libre de Bruxelles Campus Plaine. Phone :+32 2 650 53 77 Building BC, Room 1C4 203 Boulevard du Triomphe, Acces 2 1050 Brussels Belgium http://govaertslab.ulb.ac.be/

2 5

ISOLDE and secondary structure restraints
by Guido Hansen 17 Nov '23

17 Nov '23

Hi all, I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess: Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script? Cheers, Guido -- PD Dr. Guido Hansen Group Leader UNIVERSITÄT ZU LÜBECK INSTITUT FÜR BIOCHEMIE Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen(a)biochem.uni-luebeck.de www.biochem.uni-luebeck.de [1] Ratzeburger Allee 160 23562 Lübeck Links: ------ [1] http://www.biochem.uni-luebeck.de

4 5

Feature request: replace residues in model with residues from other model
by Vorländer,Matthias Kopano 16 Nov '23

16 Nov '23

Dear ChimeraX team, Thanks a lot for developing the amazing tool that is ChimeraX! I use it extensively for model building, and would like to request a functionality to replace a residue selection in one model from residues in another model (similar to what is possible in coot via the replace fragment functionality). I am aware that this currently possible by a combination of delete, combine, and changechains, but it would be great if this could be shortcutted. Many thanks in advance, Matthias

7 17

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

Re: Trouble installing plugin
by Zach Pearson 07 Sep '23

07 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/ >

3 3

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

3 12

[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

2 2

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/

5 13

ChimeraX-users August 2023