September 2023 - ChimeraX-users - RBVI Mailing Lists

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

Coloring of trajectory using mpl command
by Alexander Hung Lee 07 Sep '23

07 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

2 1

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

2 1

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

3 3

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

4 3

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.

2 1

[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

Zone map around center of rotation?
by Oliver Clarke 01 Sep '23

01 Sep '23

Hi, Surface zone allows one to carve the map in a sphere around a selected atom (with “nearAtoms”). When navigating around the map, it would be convenient to be able to use the center of rotation as a reference point instead. Would it be possible at some point to add a “nearCofR” option to surface zone to facilitate this? In Chimera, I had kind of a hack-y way to do this, by placing a marker atom at the center of rotation and using that as the reference, but this option is not yet available in ChimeraX. Cheers Oli

3 4