- ChimeraX-users - RBVI Mailing Lists

Dialog box after dockprep command in 1.7rc202311210000
by r.m.newlon＠gmail.com 22 Nov '23

22 Nov '23

Hello all, I am on an Apple M1 and have just updated to ChimeraX 1.7rc202311210000. I am just starting to learn how to use ChimeraX from the command line (Terminal). My code that ran from Terminal on ChimeraX 1.6 doesn't seem to be working now with 1.7. Specifically, it seems that the dockprep command now ends by automatically popping up a dialog box prompting you to save a Mol2 file. I think this is causing problems when I try to run in nogui mode. I will include the "error message" at the end of this message, in case it is helpful. If this dialog box is the problem, is there a way to suppress it? Thank you! RN ==== Copied from Terminal ==== ... Dock prep finished Unexpected exception, save your work and exit: Traceback (most recent call last): File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/nogui.py", line 232, in execute self._cmd.run(text) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 168, in dock_prep_cmd dock_prep_caller(session, structures, memorization=memorize, nogui=True, **kw) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 144, in dock_prep_caller run_steps(session, state, structures) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 159, in run_steps step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'], File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/prep.py", line 107, in prep callback(session, state, structures) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 159, in run_steps step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'], File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/addh/dock_prep.py", line 56, in run_for_dock_prep callback(session, state, structures) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 159, in run_steps step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'], File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/add_charge/dock_prep.py", line 58, in run_for_dock_prep callback(session, state, structures) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/cmd.py", line 154, in run_steps callback() File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/dock_prep/prep.py", line 101, in postscript show_save_file_dialog(session, format=session.data_formats.save_format_from_suffix(".mol2").name) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 138, in show_save_file_dialog _dlg.display(session, **kw) File "/Applications/ChimeraX-1.7-rc2023.11.21.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 31, in display parent = session.ui.main_window ^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'UI' object has no attribute 'main_window'

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ChimeraX-users email frequency
by Siyoung Kim 22 Nov '23

22 Nov '23

Hello, Is there a way to control the frequency of receiving emails from chimerax-users (e.g., once a day, once a week, or once a month)? Thank you. Best, Siyoung

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(no subject)
by Murphy, Kenneth 21 Nov '23

21 Nov '23

Thanks for ChimeraX. I've been loading multiple sequence alignments in fasta format directly into ChimeraX for mapping conservation onto a pdb and it works great. My MSA are directly from clustalo omega and in fasta format not clu formtat. My question is this. My compiled al2co.c as well as the binary I downloaded for al21co.exe doesn't work with input in fasta format. And yet ChimeraX opens and al2co window when I input my alignment. Does ChimeraX use another version of al2co that is configured to open fasta files? thanks for any info. ken murphy ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Sequence via remotecontrol?
by Boris Steipe 21 Nov '23

21 Nov '23

Hi all - I am using the fantastic remotecontrol REST interface in teaching, and I have hit a surprising snag: is it not possible to return the sequence of a selection through the interface? What I need to do is align fragments of sequence I have obtained from external annotations (RADAR in this case), with the SEQRES derived sequence to match the sequence numbers to each other - generally they are not the same. I think I could write FASTA to a file with "save" and process that, and I think I could capture the output of "info" and parse that through a function, but I am wondering if there is not a way to get the sequence directly as a return value? Thanks! Kind regards, Boris

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VR on/off button
by Steffen Thomas 21 Nov '23

21 Nov '23

Hello I'm currently looking into the interesting possibilities of ChimeraX and VR. As I am in a different room to my PC with my glasses, I access the PC desktop via SteamVR with ChimeraX open and start vr on in the command line. This works quite well with a virtual keyboard from SteamVR. Now I'm missing two things so far, which I probably just haven't found yet (I'm a VR newbie even though I've owned a GearView for some time now, but its capabilities are quite limited). Firstly, a virtual keyboard where I can enter commands in the command line with the blue or yellow cylinders (I have now found the command line in vr) and a button in the toolbar (for example in the Molecule Display area) that switches vr on or off, in the same way for example as show and hide ribbon. Are there any possibilities to realize this via python itself? Or plans to integrate something like this? Many thanks to the great ChimeraX community and all those responsible. Steffen --------------------------------------------------------------------------------------------------------------- Steffen Thomas

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measure rotation showAxis does not create a measurable object
by Alexis Rohou 20 Nov '23

20 Nov '23

Hello again, I have been using "measure rotation" to create several rotation axis objects, with the goal to measure angles between the various axes. Two of my axes are #4 and #5. When I try to measure the angle with "angle #4 #5", I get the error: "Must specify exactly 3 atoms/centroids or two measurable objects (e.g. axes/planes)" I notice also that the axes created by "measure rotation" do not show up in the "Structure Measurement" UI tool, which I guess is related. Would it be possible to please amend the output of the "measure rotation" command so that the axis (and slabs) it outputs are measurable? Cheers, Alexis

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Startup cxc scripts
by Siyoung Kim 20 Nov '23

20 Nov '23

Hello, Would there be a way to run some chimerax scripts at the beginning of every ChimeraX session? In particular, I want three things: 1. Change the color of the background. set bgColor white 2. Change the mode of the mouse. ui mousemode right zoom 3. Open the shell. ui tool show Shell The most relevant documentation I found was: "Python files in the directory *~/chimerax_start* (where *~* is the user's home directory) are imported automatically at startup." I put ChimeraX scripts (not python files) in this folder, but no luck. Thank you. Best, Siyoung

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Tutorial
by Mark Rosenberg 20 Nov '23

20 Nov '23

Do you have a tutorial for ChimeraX generating publication quality surface and mesh maps with a docked model, please? Thanks Dr Mark F Rosenberg

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specify id of output of define command
by Alexis Rohou 17 Nov '23

17 Nov '23

Hello, I've been scripting quite a bit with the define command of late, and I wonder if you might consider adding "id" or "modelId" to the set of general options available for this command, so that we could specify the ID of the object that is created. The current workaround is to use rename, which works but is a bit cumbersome. Given that many other commands allow us to specify ID of output objects, I figure it'd be nice for that pattern to apply here. Cheers, Alexis

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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

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