November 2023 - ChimeraX-users - RBVI Mailing Lists

How to save a sequence in an mmCIF file?
by Guillaume Gaullier 29 Nov '23

29 Nov '23

Hello, Starting from an AlphaFold prediction, I refined a model against a map with ISOLDE. I trimmed the segments not supported by any density. The resulting mmCIF file that I saved now opens with this warning: Unknown polymer entity '1' near line 187 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. Displaying the sequence of this chain shows the correct numbering (with jumps in numbering according to missing segments in the structure), but the sequence of the missing structure segments is not displayed. When I open the fasta file containing the full-length sequence, the sequence gets automatically associated to the structure, and the sequence viewer annotates the segments with missing structure correctly. I would like to save this full-length sequence in my mmCIF file so the full-length sequence with annotated missing structure segments shows up next time I open this file. But when I try to save at this point, I get the following notice: Not saving entity_poly_seq for non-authoritative sequences The documentation for "save" and "sequence" didn't help. How can I make this sequence "authoritative" and save it into my mmCIF file? Thank you in advance, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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transition dipole moments
by gennaro.pescitelli＠unipi.it 28 Nov '23

28 Nov '23

Dear developers, first of all, thnak you for your great software, I just started using it. My question: is there a way to plot transition moments (electric and magnetic), as calculated e.g. by TD-DFT calculations in ORCA or Gaussian? If not directly from a log/out file, is tehre a way to manually add a vector arrow? Thanks Rino Pescitelli

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Inquiry Regarding Feasibility of Implementing Protein Operations in Python
by g0423019 g0423019 28 Nov '23

28 Nov '23

Sorry. The earlier email by ms04000106(a)gmail.com was not sent using a university email address. It has been resent using the university email address. Dear UCSF ChimeraX, I hope this email finds you well. My name is Mayu Shibuya, and I am a student at Iwate University, currently affiliated with the wet biology laboratory. I am reaching out to seek guidance on the feasibility of utilizing the software for a specific task. Specifically, I am interested in performing addh and addcharge operations and automating these processes using a Python script. However, I do not know whether the addh and addcharge operations can be executed in Python. Could you kindly provide guidance on the possibility of achieving this with the software? If it is indeed feasible, I would greatly appreciate any instructions or methods you recommend for implementing these operations in a Python script. Thank you for taking the time to consider my inquiry. I greatly appreciate your assistance and look forward to hearing from you soon. Best regards, Mayu Shibuya Iwate University g0423019(a)iwate-u.ac.jp

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Inquiry Regarding Feasibility of Implementing Protein Operations in Python
by 澁谷まゆ 28 Nov '23

28 Nov '23

Dear UCSF ChimeraX, I hope this email finds you well. My name is Mayu Shibuya, and I am a student at Iwate University, currently affiliated with the wet biology laboratory. I am reaching out to seek guidance on the feasibility of utilizing the software for a specific task. Specifically, I am interested in performing addh and addcharge operations and automating these processes using a Python script. However, I do not know whether the addh and addcharge operations can be executed in Python. Could you kindly provide guidance on the possibility of achieving this with the software? If it is indeed feasible, I would greatly appreciate any instructions or methods you recommend for implementing these operations in a Python script. Thank you for taking the time to consider my inquiry. I greatly appreciate your assistance and look forward to hearing from you soon. Best regards, Mayu Shibuya Iwate University ms04000106(a)gmail.com

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hide dust
by Andrea Smith 28 Nov '23

28 Nov '23

Hi, I have cartoon and map visible for a part of my molecule (one protomer from a tetramer). When I click on hide dust, the dust is hidden but at the same time the map appears for the rest of the tetramer. Is there a way to hide dust around the visible part of the map while keeping a part of the map hidden? Thanks, Andrea

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(no subject)
by Murphy, Kenneth 26 Nov '23

26 Nov '23

Hi, Would there be a way to save convservation scores from a large multiple sequence alignment into a file that could be re-loaded later instead of having to reload the actual alignment file? In looking at WDFY4, the alignment of the 3124 residue protein from 523 different species, the alignment fasta file takes around 10 minutes to load. After calculating the scores, the program shows the alignment and then the showing the convervations of residues in the protein is my goal of analysis. But it takes the same 10 minutes every time I open the session. I haven't found a way to save the scores themselves and load that in directly. Is there a way to do that? thanks it's a great program. 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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Reading .xyz vs. Orca .out file
by Michael Patzschke 23 Nov '23

23 Nov '23

Dear colleagues, Recently the following problem has appeared: When I open an orca output file and chose the ball and stick option for displaying molecules, the radii of the balls are all wrong. This problem does not show up when I open the corresponding .xyz file. I try to attach an example to illustrate the problem. I would appreciate any help in this matter. Kind regards, Michael Patzschke __________________ Dr. Michael Patzschke Institute of Resource Ecology Chemistry of the f-elements Theoretical Chemistry Helmholtz-Zentrum Dresden - Rossendorf e. V. Telefon: +49 (0351) 260 2989 E-Mail: m.patzschke(a)hzdr.de <mailto:p.kaden@hzdr.de> Web: http://www.hzdr.de <http://www.hzdr.de/> Addresse: Bautzner Landstrasse 400 | 01328 Dresden Vorstand: Prof.Dr. Dr. Sebastian M. Schmidt, Dr. Diana Stiller Vereinsregister: VR 1693 beim Amtsgericht Dresden

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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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ChimeraX-users November 2023