July 2024 - ChimeraX-users - RBVI Mailing Lists

saving modifications
by Claudio Andres Aguilar Pena 23 Jul '24

23 Jul '24

Dear ChimeraX team, First of all, many thanks for the app, it’s really wonderful!. I have a question regarding one feature I would like to have and maybe it’s possible to do but I just don’t know how. I have a PDB of the structure of an enzyme that has 5 different domains: I can select the aa of each domain and give each domain a color. This is very useful for me when comparing structure predictions of the enzyme and see what happens when making mutations in the primary structure. My problem is that I cannot save the PDB with the colors for each domain, so I have to select and assign the colors every time, or leave the app and the PDB permanently open, which is not very convenient. Is there a way to save the PDB with the modifications I made? Many thanks for your help. Best, Claudio Dr. Claudio Aguilar, PhD Virologisches Institut Universität Zürich Vetsuisse Fakultät Winterthurerstrasse 266a CH-8057 Zürich Switzerland phone: +41446358712 Fax: +41446358911

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chimerax-0.1.71 python API: failed imports in module
by ishaanawasthi05＠gmail.com 22 Jul '24

22 Jul '24

Dear ChimeraX Team, I'm trying to use the ChimeraX API in python to automate some analysis. My code is not executing due to some missing/failed imports inside the ChimeraX module. File "/opt/anaconda3/lib/python3.11/site-packages/chimerax/core/models.py", line 54, in <module> from chimerax.graphics import Drawing, Pick, PickedTriangle ModuleNotFoundError: No module named 'chimerax.graphics' In the same file (models.py) there are also problems with this: "from .state import State" Together they are being used in the following class definition: class Model(State, Drawing): """ A Model is a :class:`.Drawing` together with an id number that allows it to be referenced in a typed command. .... """ I haven't been able to find any information on what these imports are, why they are missing, or how to resolve this issue. I also don't know if there are more missing imports, as it keeps failing here. I would appreciate your support in getting the Chimerax API to work — if this is the wrong place to ask, please do point me toward the right forum for ChimeraX. Thanks so much for the help!

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combining and splitting chains
by Dmitry Semchonok 22 Jul '24

22 Jul '24

Dear colleagues, I have a lot of chains that I want to combine just in 1. How to do that? And vice versa – I have 1 chain, and I want to split it into several. Thank you in advance, Kind regards, Dmitry

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ChimeraX journal-quality figures script !
by Gupta, Arun 22 Jul '24

22 Jul '24

Dear ChimeraX team, Recently, I came across this review article “Front. Microbiol.13, 2022, 891610” and I am quite fascinated by the visually appealing figures made in the above-mentioned review article. Since the figures were created with UCSF ChimeraX in the review article. I was just wondering can somebody advice or suggest what should be the specific ChimeraX command scripts for making similar journal-quality figures. Find attached one of the example figures from the review article for the reference. Thanks! Arun

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Chimerax on Fedora 40
by Vito Calderone 19 Jul '24

19 Jul '24

I have installed ucsf-chimerax-1.8-1.el9.x86_64.rpm on a fedora 40 pc. Installation was fine. When I launch 'chimerax' I get the following error: $ chimerax Fatal Python error: Segmentation fault Current thread 0x00001500f588ab80 (most recent call first): File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed File "<frozen importlib._bootstrap_external>", line 1233 in create_module File "<frozen importlib._bootstrap>", line 573 in module_from_spec File "<frozen importlib._bootstrap>", line 676 in _load_unlocked File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 1176 in _find_and_load File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/Qt/QtWebEngineWidgets.py", line 4 in <module> File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed File "<frozen importlib._bootstrap_external>", line 940 in exec_module File "<frozen importlib._bootstrap>", line 690 in _load_unlocked File "<frozen importlib._bootstrap>", line 1147 in _find_and_load_unlocked File "<frozen importlib._bootstrap>", line 1176 in _find_and_load File "<frozen importlib._bootstrap>", line 241 in _call_with_frames_removed File "<frozen importlib._bootstrap>", line 1232 in _handle_fromlist File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/Qt/__init__.py", line 112 in qt_have_web_engine File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/ui/gui.py", line 108 in __init__ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 653 in init File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1166 in <module> File "<frozen runpy>", line 88 in _run_code File "<frozen runpy>", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._p cg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets (total: 18) Segmentation fault (core dumped) Any hint? Thanks Vito -- Dr. Vito Calderone Ph.D. Associate Professor of Inorganic Chemistry CERM and Department of Chemistry University of Florence Via Luigi Sacconi, 6 50019 Sesto Fiorentino (FI) Italy tel: +39 055 457 4276

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sequence identity command
by NUR AIDA SAKINAH 18 Jul '24

18 Jul '24

Hai, I want to use the sequence identity command in ChimeraX but in the log said "Missing or invalid "src1" argument: Expected alignment-id or [alignment-id]:sequence-name-or-number". The input I gave is "sequence identity alignment-1" after open the tools>sequence>show sequence viewer and then select model e.g. #1/a and it show the ID as [ID: 1] but i got error. How to solve this problem? Hope ChimeraX teams can help. Thank you!

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ChimeraX 1.8 linux download options
by Elaine Meng 17 Jul '24

17 Jul '24

Dear Charitha Shetty, Please send ChimeraX general support questions to chimerax-users(a)cgl.ucsf.edu (not chimera(a)cgl.ucsf.edu) as those of us on the commercial licensing team may not know the technical details. My recollection is that flatpak is supposed to work better in a broader set of situations than generic linux, but this is not my area of expertise so I am also forwarding this question to the chimerax-users list where linux experts may wish to correct me or add more details. When you send a message to the list in the future, be careful not to include any proprietary information, including your license key, since your message will be seen by others on the list and included in the public archive of past messages. Regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco > Begin forwarded message: > > From: Charitha Belluru Shetty <charitha-belluru.b.shetty(a)gsk.com> > Subject: RE: Commercial Software Download and License key? > Date: July 16, 2024 at 5:04:37 PM PDT > To: Amrit Sukheja <Amrit.Sukheja(a)netascientific.com>, "'Cantero, Kimberly'" <Kimberly.Cantero(a)ucsf.edu>, Amey Kanitkar <amey.p.kanitkar(a)gsk.com>, Jim Thorpe <james.h.thorpe(a)gsk.com> > Cc: Ye Che <ye.x.che(a)gsk.com>, Chun-wa Chung <chun-wa.h.chung(a)gsk.com>, Mustapha Gbassa <Mustapha.Gbassa(a)netascientific.com>, "chimera(a)cgl.ucsf.edu" <chimera(a)cgl.ucsf.edu>, Andrew Verlander <Andrew.Verlander(a)netascientific.com> > > Hi Chimera Team, > > We are trying to download the latest version 1.8 for Centos 7. Do you guys have the Generic Linux 64-bit version for it, as available for 1.7 (screenshot 2)? > 1.8 version shows below option and cannot see a tar.gz as 1.7 version. Can you please provide a link from where we can download the tar.gz for the 1.8 tar.gz version. Thank you in advance! > > Screenshot 1: > > > > Screenshot 2: > https://www.rbvi.ucsf.edu/chimerax/older_releases.html <https://www.rbvi.ucsf.edu/chimerax/older_releases.html> > > > > Best Regards, > Charitha Shetty

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Question about automating with ChimeraX in Visual Studio Code
by Eric Pettersen 17 Jul '24

17 Jul '24

> Begin forwarded message: > > From: chimerax-users-owner(a)cgl.ucsf.edu > From: Yue Bao <nkby(a)outlook.com <mailto:nkby@outlook.com>> > Subject: Question about automating with ChimeraX in Visual Studio Code > Date: July 15, 2024 at 11:54:25 PM PDT > To: "chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>" <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> > > > Hi, > > I am using ChimeraX to visualize a list of protein structures, including hiding/showing/coloring specific chains (sometimes amino acids specific). Because I have a long list, I wanted to get it done not with the ChimeraX console but with Visual Studio Code, since you provided python APIs. > > N.B. I can do run(session, 'open 6qzp') in the Qt console in ChimeraX, as session has been loaded. It is good, just not as efficient as running in VS code. > > However, in VS code it is not working. Here are my code and error messages. Is it because I didn't setup the standalone environment correctly? If possible, could you help me with a piece of sample code and the documentation? > > best, > Yue > --- > > interpreter I used > /Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/bin/python3.11 > > I have a script basically to open a PDB structure and get some visualizations done > > from chimerax.core.session import Session > > from chimerax.core.commands import run > > > def main(): > > session = Session('chimerax') > > run(session, 'open 6qzp') > > run(session, 'hide atom') > > run(session, 'show cartoon') > > run(session, 'select #1') # select all proteins > > run(session, 'color #AAAAAA All') > > run(session, 'select #0') > > main() > > when I run it in VS code, it gives me some error > run(session, 'open 6qzp') > File > "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- > packages/chimerax/core/commands/run.py", line 49, in run > results = command.run(text, log=log, return_json=return_json) > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > File > "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- > packages/chimerax/core/commands/cli.py", line 2849, in run > _compute_available_commands(session) > File > "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- > packages/chimerax/core/commands/cli.py", line 2431, in > _compute_available_commands > ts.register_available_commands(session.logger) > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > AttributeError: 'NoneType' object has no attribute > 'register_available_commands' > > > BUG: AttributeError: 'NoneType' object has no attribute > 'register_available_commands' > > File > "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- > packages/chimerax/core/commands/cli.py", line 2431, in > _compute_available_commands > ts.register_available_commands(session.logger) > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > > _See log for complete Python traceback._ >

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Coloring aligned structures by RMSD
by Chen, Daphne 16 Jul '24

16 Jul '24

Hello, I have a large ChimeraX session containing homologs of my protein of interest (~120 PDB files in one session). I’ve been able to align them using MatchMaker, but I noticed that I have to check the “Show pairwise sequence alignments” box under “Alignment” in the Matchmaker window if I want to color by RMSD in the Render by Attribute menu. Is there a way to color by RMSD without displaying all the pairwise sequence alignments? Whenever I try to open my session, there are so many pairwise alignment windows that have to be loaded that ChimeraX ends up crashing. Thanks, Daphne

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How to add calcium ions into a predicted protein structure
by MARIAM ALZAABI 16 Jul '24

16 Jul '24

Dear Sir, How to add calcium ions into a predicted protein structure that I created using alpha fold colab in chimeraX Thank you.

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