December 2023 - ChimeraX-users - RBVI Mailing Lists

Error in using alphafold by ChimeraX
by Ping-Hung Chen 陳炳宏 25 Dec '23

25 Dec '23

Hi, I tried to run Alphafold prediction by ChieraX, and it appears below Error. Please cite ColabFold: Making protein folding accessible to all. Nature Methods (2022) if you use these predictions. INFO:__main__:Starting prediction on 2023-12-26 UTC time INFO:__main__:Installing ColabFold on Google Colab virtual machine. --------------------------------------------------------------------------- ImportError Traceback (most recent call last) <ipython-input-8-1833a07b73e1> in <cell line: 329>() 327 remove_from_list(seq_list, 'prokaryote') # Obsolete "prokaryote" flag 328 --> 329 run_prediction(seq_list, use_templates = use_templates, energy_minimize = not dont_minimize) 7 frames /usr/local/lib/python3.10/dist-packages/alphafold/data/mmcif_parsing.py in <module> 22 from absl import logging 23 from Bio import PDB ---> 24 from Bio.Data import SCOPData 25 26 # Type aliases: ImportError: cannot import name 'SCOPData' from 'Bio.Data' (/usr/local/lib/python3.10/dist-packages/Bio/Data/__init__.py) --------------------------------------------------------------------------- Would you like to help me with it? Thank you. Sincerely, PH Ping-Hung Chen, Ph.D., Assistant Professor Institute of Biochemistry and Molecular Biology College of Medicine, National Taiwan University Address: R913, No.1, Sec.1, Ren-Ai Rd., Zhongzheng Dist., Taipei 10051, Taiwan (R.O.C.) E-mail: pinghungchen(a)ntu.edu.tw; phcrose(a)gmail.com Phone: +886 2-23123456 Ext. 88864

3 2

Re: How to save a sequence in an mmCIF file?
by Greg Couch 22 Dec '23

22 Dec '23

To answer the general question, ChimeraX doesn't yet have a way to set the full sequence for a mmCIF entity. See https://www.wwpdb.org/deposition/preparing-pdbx-mmcif-files for how to fix the mmCIF output from various refinement packages. For example, the Phenix has "mmtbx.prepare_pdb_deposition program to create a mmCIF file with the sequence". In this particular case, where the starting structure is an Alphafold prediction with atoms for every residue in the full sequence, you can get the correct sequence into the mmCIF output with the "bestGuess" option. See https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#mmcif. I'd also recommend, in your case, using the computedSheets option. In older ChimeraX's, you need to run dssp before using computedSheets to get the helix information. In recent ChimeraX's (daily build and 1.7 release candidate), computedSheets will also output the helix information if it wasn't present in the input. Adding a sequence with bestGuess can be deceiving of because missing leading or trailing residues, or gaps of indeterminate length. But in this case, you should be fine. -- Greg On 11/29/23 02:45, Guillaume Gaullier wrote: > *From: *Guillaume Gaullier via ChimeraX-users > <chimerax-users(a)cgl.ucsf.edu> > *Subject: **[chimerax-users] How to save a sequence in an mmCIF file?* > *Date: *November 29, 2023 at 2:45:31 AM PST > *To: *"chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> > *Reply-To: *Guillaume Gaullier <guillaume.gaullier(a)kemi.uu.se> > > 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_______________________________________________ > ChimeraX-users mailing list --chimerax-users(a)cgl.ucsf.edu > To unsubscribe send an email tochimerax-users-leave(a)cgl.ucsf.edu > Archives:https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl… >

6 18

autodock Vina
by Michael Sacher 22 Dec '23

22 Dec '23

I am running Chimera X. I downloaded autodock Vina. It should show as a tool>surface binding analysis but it is not there. How do I get the surface binding analysis option to show and to display Vina? Thanks. Michael

2 3

Cannot launch ChimeraX 1.7 GUI on Red Hat Enterprise Linux 9.3
by Wen 21 Dec '23

21 Dec '23

Dear Elaine, I tried to install ChimeraX 1.7 on Red Hat Enterprise Linux 9.3. yum install mesa-libOSMesa-21.3.4-2.el9.x86_64.rpm yum install ucsf-chimerax-1.7-1.el9.x86_64.rpm Everything went well. However, when I tried to launch ChimeraX, I met the following errors: [wenliu@localhost Downloads]# chimerax QStandardPaths: runtime directory '/run/user/800' is not owned by UID 0, but a directory permissions 0700 owned by UID 800 GID 800 QStandardPaths: runtime directory '/run/user/800' is not owned by UID 0, but a directory permissions 0700 owned by UID 800 GID 800 NOTE: available bundle cache has not been initialized yet NOTE: 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/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/__main__.py", line 1069, in <module> exit_code = init(sys.argv) ^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/__main__.py", line 664, in init toolshed.init(sess.logger, debug=sess.debug, File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 1389, in init _toolshed = Toolshed(*args, **kw) ^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/toolshed/__init__.py", line 396, in __init__ settings.toolshed_last_check = now.isoformat() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/settings.py", line 199, in __setattr__ ConfigFile.__setattr__(self, name, value) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/configfile.py", line 386, in __setattr__ ConfigFile.save(self) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/configfile.py", line 335, in save with SaveTextFile(self._filename) as f: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/safesave.py", line 191, in __init__ SaveFile.__init__(self, filename, open=open_text, critical=critical) File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/safesave.py", line 80, in __init__ raise OSError(errno.ENOTDIR, os.strerror(errno.ENOTDIR), save_dir) NotADirectoryError: [Errno 20] Not a directory: '/do/not/run/as/root/.config/ChimeraX' BUG: NotADirectoryError: [Errno 20] Not a directory: '/do/not/run/as/root/.config/ChimeraX' File "/usr/libexec/UCSF-ChimeraX/lib/python3.11/site- packages/chimerax/core/safesave.py", line 80, in __init__ raise OSError(errno.ENOTDIR, os.strerror(errno.ENOTDIR), save_dir) _See log for complete Python traceback._ ChimeraX did not launch. Could you advise me on how to proceed? Thanks in advance. Wen Liu @ UCHC

2 1

ISOLDE 1.7 released
by Tristan Croll 21 Dec '23

21 Dec '23

Hi all, To follow the recent announcement of the ChimeraX 1.7 release, I'm happy to announce the matching release of ISOLDE 1.7. Should now be available for installation from the ToolShed. I've also put up a new build of the QScore plugin compatible with Python, allowing it to be used with recent ChimeraX versions. Happy holidays (and happy modelling)! Best, Tristan -- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT

1 0

ChimeraX Log File Question
by Bani Kaur 20 Dec '23

20 Dec '23

Hi, I hope you are doing well! My name is Bani Kaur and I am a ChimeraX user. I wanted to ask you how I would be able to download my log file - I am not able to figure out what line to put into the system. Thank you so much! Best, Bani kaur

2 2

ChimeraX protein-protein binding site modeling question
by Parks, Ryssa 20 Dec '23

20 Dec '23

Hello, I work in a lab that researches biopesticides in the form of insect neuropeptides, which bind to receptor proteins. I am trying to use ChimeraX to model potential binding sites between peptide ligands and their corresponding receptor. Does ChimeraX have this capability? When I was trying to figure this out myself online through the ChimeraX Youtube tutorials and tutorials on the UCSF site, I came across a comment on a video that mentioned I could upload the sequences of my receptor and peptide ligand separated by a comma, and model it as a protein complex, and then I can get information on where the two molecules interact. I'm relatively new to protein research, and so I hadn't yet thought of ligand-protein interactions as a type of protein complex. My specific questions are: * When modeling a peptide ligand and a receptor as a protein complex, will ChimeraX accurately predict the relationship between the two molecules based on binding compatibility? Or is it based on something else, like similarity of sequence alignments...? * If multiple binding sites are possible, is there any way to view the different options for multiple binding sites? Or is there any way to restrict the area on the receptor to which my target peptide ligand is predicted to bind (i.e. the extracellular region only)? * The peptide ligands are only 7-9 amino acids in length and do not take very long to model, but the receptor is about 600 amino acids and takes a much longer time to model. Do I have to model protein complexes by re-modeling everything for each different receptor-ligand combination, or can I combine existing models somehow? I hope these questions aren't too troublesome, and I hope I haven't grossly misunderstood ChimeraX's capabilities. Thank you for your time, Ryssa Parks

3 2

Problem with Snap Installation
by Stephen P. Molnar 20 Dec '23

20 Dec '23

I have had Chimerax.flatpack installed on by Debian Bookworm Platform. As a result of a system crash I was force to reinstall the OS. When I attempted a reinstallation on the New OS I got the following error: error: The application edu.ucsf.rbvi.ChimeraX/x86_64/master requires the runtime org.freedesktop.Platform/x86_64/22.08 which was not found Please advise. Thanks in advance. -- Stephen P. Molnar, Ph.D. https://insilicochemistry.net (614)312-7528 (c) Skype: smolnar1

3 5

ISOLDE messes with view?
by Alexis Rohou 19 Dec '23

19 Dec '23

Hello, I've just noticed that the view command doesn't behave as expected after I have started ISOLDE. Specifically, if I save a view ("view name view1") and later try to restore it ("view view1"), it will get me back to the correct orientation of view1 but the zoom will not be restored. I assume ISOLDE is changing a setting under the hood. Is there some way to make ISOLDE play nicely with "view"? Right now my only workaround is to quit ChimeraX and start again front he beginning, without launching ISOLDE. Cheers, Alexis

3 9

Adjust Torsions section of Build Structure is missing
by duhq 19 Dec '23

19 Dec '23

3 4

ChimeraX-users December 2023