- ChimeraX-users - RBVI Mailing Lists

ChimeraX / Alphafold docking question: Heterodimer and ligand
by Anthony Newcombe 08 May '24

08 May '24

Hello I'm currently evaluating ChimeraX for non-commercial use. I'm interested in predicting a complex of an unknown ligand to a heterodimer (receptor) with a known structure, pdb file available. The help files mention: *For predicting a complex (multimer), the sequences of all chains in the complex must be given. The same sequence must be given multiple times if it occurs in multiple copies in the complex. The sequences can be specified either collectively as a model number chosen from the menu of currently open models (e.g. when that model contains multiple chains)* If I download the structure of the heterodimer first, does this mean I can then select this then add the primary sequence of the ligand to try to dock? If not, can I add all the primary sequences and tick 'use PDB templates when predicting structures'? Would this then use the known experimental structure of the receptor? I hope this makes sense and thanks for the help Best wishes Tony Anthony Newcombe Ballinascarthy Clonakilty Cork Ireland

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Fwd: registration issue
by Elaine Meng 08 May '24

08 May '24

Hi Stephen, For questions that don't relate directly to commercial licensing, please use chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (already CC'd here so you don't need to do it) or chimerax-bugs(a)cgl.ucsf.edu <mailto:chimerax-bugs@cgl.ucsf.edu> .... I don't know the answer to your question but the people on those lists would be your best bet. See the "contact us" page: <https://rbvi.ucsf.edu/chimerax/docs/contact.html <https://rbvi.ucsf.edu/chimerax/docs/contact.html>> If I had to guess, I would say that our server was temporarily down and that as soon as it is up (which may actually be the case), your registration attempt will "take" and you won't be prompted again in the near future. As the dialog says, please try again, although I know it's annoying if the server is still down. Maybe somebody on our team can respond as to whether it is up now? In the meanwhile, very sorry for the inconvenience and wasted time filling out the form. Best 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 > From: Stephen Miller <miller.stephen(a)gene.com <mailto:miller.stephen@gene.com>> > Sent: Monday, May 6, 2024 3:14 PM > Subject: registration issue > > Hello, I use a ChimeraX license through Genentech, and recently had to swap out my computer due to an issue and had to reinstall the program. I've been getting a notification to register but when I submit the information it says the registration > ZjQcmQRYFpfptBannerStart > This Message Is From an External Sender > This message came from outside your organization. > ZjQcmQRYFpfptBannerEnd > Hello, > > I use a ChimeraX license through Genentech, and recently had to swap out my computer due to an issue and had to reinstall the program. I've been getting a notification to register but when I submit the information it says the registration server is unavailable, and then the notification pops up the next time I launch the program. > > Is there something I can do to get this done properly? Thank you for any help! > -Steve > >

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Re: [Chimera-users] Chimera scripting
by Elaine Meng 07 May '24

07 May '24

Hi Flip, If you save a PDB file from ChimeraX it will save the current helix and strand assignments of the protein and peptide residues (as HELIX and SHEET records). I'm not sure if that is what you were saying is missing, or how you determined that they were missing. It does not save, however, helix type or which sheets the strands belong to. Elaine > On May 7, 2024, at 11:29 AM, Flip Jansen <f.bastiaanjansen(a)gmail.com> wrote: > > Hi Elaine, > > Thank you that is very clear! > > As for the second point, I meant preserving secondary structure information when saving an adapted PDB file in Chimera. I am now planning on using PyMOL for this purpose. > > Thanks again for your help! > > Best, > Flip > > On Mon, May 6, 2024 at 11:56 AM Elaine Meng <meng(a)cgl.ucsf.edu> wrote: > Hello Flip, > (1) we would generally recommend using ChimeraX over Chimera for many reasons: performance, enhanced features, current development and support. The rest of this answer applies to ChimeraX so I'm putting it on the chimerax-users list. > > (2) you can create a blank cubic grid first with "volume new" and then refer to that in the "molmap" command "onGrid" option. > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#new> > <https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html> > > (3) I do not understand what you mean by losing secondary structure information when saving a map. Only atomic structures (not maps) have secondary structure information, i.e. helix and strand assignments. Can you clarify? > > I hope this helps, > Elaine > ----- > Elaine C. Meng, Ph.D. > UCSF Chimera(X) team > Department of Pharmaceutical Chemistry > University of California, San Francisco > > > On May 6, 2024, at 10:40 AM, Flip Jansen via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > > > Hello Chimera dev team, > > > > I am a junior specialist from across the hall working at the Fraser Lab and I have some questions about using chimera scripting for omitting densities and generating reference maps. > > > > One of the issues I have been having has been that using the molMap function in Chimera generates a non-cubic output and I am aware that I can use onGrid with a pre-existing map with the desired dimensions. However, in the workflow, I am setting up I do not yet have a reference map and I am in most scenarios starting with just a PDB or an adapted from PDB map. > > > > Is there a way to let Chimera(X) generate a cubic output map from PDB without requiring another map from an external program like cryoSPARC? > > > > Another question I have is regarding the loss of secondary structural information when saving a map in Chimera. Is there a way to save a map while maintaining that information? > > > > Any help is highly appreciated, I would also be happy to come by an talk in person. > > > > Best, > > Flip Jansen >

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Guidance on aligning models with overlapping aa subsequences
by Martin Gordon 07 May '24

07 May '24

Hi everyone, I'm hoping to get some assistance from the community for visualizing structures from multiple AF runs with overlapping subsequences. We have been using AlphaFold monomer to try to identify structure and domains of a large (+3000aa) human protein. Our AF runs fail to model the full structure (possibly insufficient resources), so we have tried 'breaking' up the protein into overlapping subsequences. I was wondering if there is a sensible way to combine these substructures based on their overlapping regions? I have tried matchmaker, which I believe constructs a MSA and attempts to align the structures, but it seems a significant region of the overlap is not aligning correctly (img below with the overlapping subsequences highlighted). Any guidance is greatly appreciated. Thank you, Martin [image: image.png] Thank you, Martin

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Inquiry on the vertex_convexity function
by Yoseph Loyd 07 May '24

07 May '24

Hi ChimeraX Team, My name is Yoseph, I'm a student. I saw that your measure convexity function 'vertex_convexity' is documented to report the vertex convexity from ' 2pi - half cone angle of the incident vertex and all triangles the incident vertex is a part of'. Is the half cone angle generated by averaging all half cone angles? Thank you for taking the time to read this and I hope your day goes well. Best regards, Yoseph Loyd

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Making movie of whole cell model with EM images
by George Schaible 07 May '24

07 May '24

Hello, My name is George Schaible and I am a post doc at Montana State University. I would like to use ChimeraX to make my movies of whole cell serial block face EM data I have modeled in IMOD/3dmod and I was wondering if someone could point me towards a tutorial or some way that I can make the movie using both the model and the original EM data. Any information is helpful and thank you! -- George A. Schaible, Ph.D Dept. of Chemistry & Biochemistry Montana State University Google Scholar profile <https://scholar.google.com/citations?user=_M2xvYIAAAAJ&hl=en>

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No version number in Add- Remove Program (Windows)
by Gruhm, Sebastian 07 May '24

07 May '24

Hello, I manage the software distribution at the Frei Universität Berlin, and I noticed that after installing ChimeraX 1.7.1, the entry in "Add-Remove Programs" (ARP) does not include a version number (see attached Screenshot). This is problematic because I cannot create a query for the version number in the software distribution (SCCM). All that would need to be done to display the version number under ARP is to create the RegKey "DisplayVersion" under "HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall\UCSF ChimeraX_is1". Would be great to see this implemented in the next version of ChimeraX. Mit freundlichem Gruß Sebastian Gruhm [cid:image001.jpg@01DAA061.0DA8A940] Zentraleinrichtung für Datenverarbeitung Server Infrastructure (SI) Fabeckstraße 32, 14195 Berlin Raum: 110 Phone: +49 30 838 58668 sebastian.gruhm(a)fu-berlin.de

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Adjust the Rotation Axis Size in ChimeraX
by AARON FERRELL 07 May '24

07 May '24

Hello, Is there a way to adjust the size of the rotation axis generated by the command line "measure rotation #2 toModel #1, in ChimeraX? I am looking to adjust both the length and diameter of the axis display. Please let me know! Best, Aaron

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Issue with Recurring Update Notifications in ChimeraX
by ahmed morsy 07 May '24

07 May '24

Dear ChimeraX Support Team, I hope this message finds you well. I am writing to ask for help with an ongoing issue I've been having with ChimeraX. Despite having downloaded and installed the most recent version of ChimeraX, I continually receive prompts to update the software each time I launch it. This occurs even though I am certain I am running the latest version. Could you please help me understand why this might be happening, and advise on how to resolve this issue? It would be helpful if you could provide steps or recommendations to ensure that the software recognizes the current version installed on my system. Thank you for your time and assistance. I look forward to your prompt response. Best regards,Ahmed Morsy=========================Ahmed Morsy, Ph.D. Assistant Professor, Department of Stem Cell & Regenerative Biotechnology,Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, KoreaTel.: 02-450-0498C.P.: +82/10-5299-5844E-mail: ahmed_morsy86(a)yahoo.com; ahmed(a)konkuk.ac.kr Orcid id: https://orcid.org/0000-0003-3873-9903 Scopus id: 55258308400 (https://www.scopus.com/authid/detail.uri?authorId=55258308400) Researchgate: https://www.researchgate.net/profile/Ahmed-Abdal-Dayem GoogleScholar: https://scholar.google.co.kr/citations?user=NevFBgMAAAAJ&hl=en

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Alphafold
by Chang, Jufang 07 May '24

07 May '24

Dear Sir Recently I can not use the ChimerX to do the alphafold prediction. The error message is some connection to the colab is broken sine March 2024. I am wondering when this feature of ChimeraX will come back? Thank you Ju-Fang ________________________________ 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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Amber output pdb file - can't open... bad PDB record
by Alexander Hung Lee 06 May '24

06 May '24

Hi! I have a large system containing >100k atoms w/o water. Amber produced a pdb file, and I have a trajectory file for it. When I try to open the pdb in chimeraX, most of it loads but with warning "Ignoted bad PDB record on line xxx" and it's all for atom # > 9,999. As a result, when I try to open the .nc file along with the pdb file, the # of atoms don't match anymore. Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

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Re: [Chimera-users] Chimera scripting
by Elaine Meng 06 May '24

06 May '24

Hello Flip, (1) we would generally recommend using ChimeraX over Chimera for many reasons: performance, enhanced features, current development and support. The rest of this answer applies to ChimeraX so I'm putting it on the chimerax-users list. (2) you can create a blank cubic grid first with "volume new" and then refer to that in the "molmap" command "onGrid" option. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#new> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/molmap.html> (3) I do not understand what you mean by losing secondary structure information when saving a map. Only atomic structures (not maps) have secondary structure information, i.e. helix and strand assignments. Can you clarify? I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 6, 2024, at 10:40 AM, Flip Jansen via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello Chimera dev team, > > I am a junior specialist from across the hall working at the Fraser Lab and I have some questions about using chimera scripting for omitting densities and generating reference maps. > > One of the issues I have been having has been that using the molMap function in Chimera generates a non-cubic output and I am aware that I can use onGrid with a pre-existing map with the desired dimensions. However, in the workflow, I am setting up I do not yet have a reference map and I am in most scenarios starting with just a PDB or an adapted from PDB map. > > Is there a way to let Chimera(X) generate a cubic output map from PDB without requiring another map from an external program like cryoSPARC? > > Another question I have is regarding the loss of secondary structural information when saving a map in Chimera. Is there a way to save a map while maintaining that information? > > Any help is highly appreciated, I would also be happy to come by an talk in person. > > Best, > Flip Jansen

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session files question
by Krishnan Raman 06 May '24

06 May '24

I have two large session files (1-2 GB). Is there any way to combine them ? thanks Krish CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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Error when opening multiple tiff stacks (32-bit)
by Christophe Leterrier 03 May '24

03 May '24

Hi, I have two 32-bit tiff stacks (generated by ImageJ) and I try to open both to overlay two channels. When opening the second one or trying to open both at the same time (see paths below), I get the following error with the latest stable and daily ChimeraX macOS versions: UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX open "/Users/christo/Travail/Data NSTORM/230811 Patt#56/Figure 4 Article (actin DNA-Paint bass)/3um aligned 3D/Recs TS ROIs 3um aligned (Gxy4z4)/Roi002_C2_N04_ch1_ph647_bas643_sypto_map_3D_48K_DC1C_(22688,12672)_TS3D.tif" "/Users/christo/Travail/Data NSTORM/230811 Patt#56/Figure 4 Article (actin DNA-Paint bass)/3um aligned 3D/Recs TS ROIs 3um aligned (Gxy4z4)/Roi002_C2_N04_ch2_ph647_bas643_sypto_map_3D_7,63K_DC1C_transfo_(22688,12672)_TS3D.tif"Traceback (most recent call last): File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py", line 334, in _qt_safe run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + ("" 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 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 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 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 191, in provider_open models, status = collated_open(session, None, paths, data_format, _add_models, log_errors, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 513, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/__init__.py", line 182, in open return open_map(session, path, format=_name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 3621, in open_map smodels, smsg = open_grids(session, sgrids, name, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 3723, in open_grids v.update_drawings() File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 813, in update_drawings self.image_levels, self.image_colors = self.initial_image_levels() ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 633, in initial_image_levels mstats = self.matrix_value_statistics() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 1734, in matrix_value_statistics matrices = self.displayed_matrices(read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 1769, in displayed_matrices matrices.append(self.matrix(read_matrix)) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 1252, in matrix m = self.region_matrix(r, read_matrix) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map/volume.py", line 1276, in region_matrix m = d.matrix(origin, size, step, progress, from_cache_only) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map_data/griddata.py", line 317, in matrix m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map_data/imagestack/imagej_tiff.py", line 74, in read_matrix a = pi.planes_data(klist, cc, ch, self.time) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/map_data/imagestack/imagej_tiff.py", line 199, in planes_data a = tif.asarray(key = plist) ^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py", line 4272, in asarray pages = pages._getlist(key) ^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py", line 7532, in _getlist pages = [getitem(i, validate=validhash) for i in key] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py", line 7532, in <listcomp> pages = [getitem(i, validate=validhash) for i in key] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py", line 7578, in _getitem self._seek(key) File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py", line 7481, in _seek raise IndexError('index out of range') IndexError: index out of range IndexError: index out of range File "/Applications/ ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/tifffile/tifffile.py", line 7481, in _seek raise IndexError('index out of range') See log for complete Python traceback. Any idea of what is going wrong?

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[Query] Possible to control tool panel size programmatically?
by leeyang+chimerax＠gmail.com 03 May '24

03 May '24

Hi, Not a feature request but a query. Is there currently a way to change tool panel sizes with a command, either in absolute terms or as a fraction of another parameter value? Cheers, Yang

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Installing ChimeraX on Ubuntu 24.04 LTS
by mborgnia＠gmail.com 03 May '24

03 May '24

Hi all, I got a shiny new machine with Ubuntu 24.04 LTS, unfortunately the regular repositories do not include libffi7 and that causes a failure when installing the 22.04 package. I have also tried to run the generic Linux 64 bit version but fails to load because the libffi.so.6 file is not found. Any ideas on how to proceed? Thanks Mario J. Borgnia

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Using chimerax library code outside of the GUI
by Artie Kushner 03 May '24

03 May '24

Hi, I apologize sincerely since I imagine this comes up often on the mailing list. I'm basically wondering if it's possible to import just the `core` functionality from a chimerax installation into a custom python environment and bypass the GUI and the binary completely. Example: I don't think it matters whether it's linux, mac, or source build, but let's say i installed a clean chimerax via my package manager (`yay i chimerax`). It's at `/opt/chimerax` and looks like this: (venv) ᢹ ritual.rtviii[ /opt/chimerax ] ls -la total 24 drwxr-xr-x 6 root root 4096 May 1 16:08 . drwxr-xr-x 10 root root 4096 May 1 16:58 .. drwxr-xr-x 4 root root 4096 May 1 16:51 bin drwxr-xr-x 8 root root 4096 May 1 16:51 include drwxr-xr-x 4 root root 4096 May 1 16:51 lib drwxr-xr-x 6 root root 4096 May 1 16:51 share If I launch `chimerax` at the command line, i get a functional GUI etc. It works. I create a fresh custom `virtualenv` with the same python that this chimerax ships: virtualenv --python='/opt/chimerax/bin/python3.11' venv Then i do something ugly in the name of science: i symlink the chimerax folder from the installation into my virtualenv: ln -s /opt/chimerax/lib/python3.11/site-packages/chimerax /home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-packages/chimerax i also tried: for P in $(ls /opt/chimerax/lib/python3.11/site-packages/); do ln -s /opt/chimerax/lib/python3.11/site-packages/$P /home/rtviii/dev/try_chimerax/ venv/lib/python3.11/site-packages/$P; done This enables me to import chimerax modules into my python code that uses this virtualenv: ```/home/rtviii/dev/try_chimerax/test.py from chimerax.core.commands import run from chimerax.core.session import Session import chimerax.mmcif.mmcif as mmcif s = Session("Hi") print(s) run(s,"open 1ubq.cif") ``` However, this is where i'm struggling a little to use any actual functionality (especially interested in cutting, merging structures and operations treating density maps and mmcif structures) because the Session wouldn't initialize well: ``` <chimerax.core.session.Session object at 0x70472673b5d0> NOTE: Traceback (most recent call last): File "/home/rtviii/dev/try_chimerax/test.py", line 9, in <module> run(s,"open 1ubq.cif") File "/home/rtviii/dev/try_chimerax/venv/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 "/home/rtviii/dev/try_chimerax/venv/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2849, in run _compute_available_commands(session) File "/home/rtviii/dev/try_chimerax/venv/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 "/home/rtviii/dev/try_chimerax/venv/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._ ``` I had some success with a similar approach in PyMol in this regard, but can't quite get this to work in ChimeraX. I really appreciate any advice for achieving this scripting decoupling from GUI/binary if that's possible at all: - either how to "pull in" ChimeraX library code properly (i realize mine is an ugly hack) - how to use library code otherwise - how to bypass the dependence of a lot of commands on the Session object or how to initialize it outside of the gui properly: an example of how to use selections to open a local density map and perform a smoothing, for example. Kindest regards and huge thanks for the monumental application. Artem, UBC Vancouver

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Problem visualizing hydrogen bonds during a trajectory
by Ute Roehrig 02 May '24

02 May '24

Hello, I'm trying to visualize the hydrogen bonds of a small molecule in water over the trajectory of a molecular dynamics simulation, using the following commands: alias evalhb hide solvent; hb :LIG reveal true coordsets false makePseudobonds true ; view perframe evalhb; coordset #1 1,20 holdsteady :LIG; wait 20; ~perframe However, this does not work as expected. Could you please help me with this issue? Thank you, Ute

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Visualizing PAE contact lines between more than two peptides
by David S. Fay 30 Apr '24

30 Apr '24

Greetings, Was wondering if it’s possible to simultaneously display PAE contact lines for more than two peptides? For example, all contacts between A and B AND B and C etc. Couldn’t find anything on it and have already made the obvious attempts such as "alphafold contacts /A to /C AND /B to /C distance 6” Thanks! David

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Schematic
by Das, Abhinaba 30 Apr '24

30 Apr '24

Hi all, I don’t think it is possible to draw this kind of schematic representation (panel b) in ChimeraX, is it? [cid:image001.png@01DA9A41.C6E2E040] Thanks, Abhi

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Alphafold predicton using ChimeraX
by Chang, Jufang 29 Apr '24

29 Apr '24

Dear Sir, When I tried to use alphafold prediction with ChimeraX, I got this error message. I alreday download the latest version 1.7.1 (2024-01-23). But I still got the same error message. Could you please suggest me what to do the next to fix this? Thank you Ju-Fang AlphaFold Prediction Requires Newer ChimeraX Alphafold prediction requires a ChimeraX daily build from March 19, 2024 or later. The ChimeraX AlphaFold prediction service was broken by an update on Google Colab on March 14, 2024. ________________________________ 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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running AlphaFold predictions in ChimeraX
by Elaine Meng 29 Apr '24

29 Apr '24

> On Apr 29, 2024, at 9:31 AM, Chang, Jufang via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear Greg > > Recently I can not use the ChimerX to do the alphafold prediction. The error message is some connection to the colab is broken sine March 2024. I am wondering when this feature of ChimeraX will come back? > > Thank you > > Ju-Fang Hello Ju-Fang, As Greg said, you should use the address chimerax-users(a)cgl.ucsf.edu for ChimeraX questions, not chimera-users(a)cgl.ucsf.edu which is for Chimera, and put some description of the current issue in the email subject line. If you get an error running the AlphaFold prediction in ChimeraX and you think it is a bug, please use ChimeraX menu Help... Report a Bug and include a description and your email address. As far as I knew it was working, so we wouldn't know what the problem is for you without more information. Also here are some common issues and limitations of running these predictions: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/alphafold.html#caveats> I hope this helps, 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

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Unroll radius?
by Ricardo Righetto 29 Apr '24

29 Apr '24

Hi, We've been using the 'volume unroll' command on a cylindrical structure, and while we do get some very decent results with the defaults, we want to do a systematic comparison with values entered manually for the inner and outer radius. Specifically, I'd like to know if I can get ChimeraX to report what minimum and maximum radii it is currently using for unrolling the volume? Currently, all I get in the reply log is this: volume unroll #1 Opened unrolled SPA_density.mrc as #2, grid size 68,697,492, pixel 1.22,1.2,1.2, shown at step 1, values float32 https://www.cgl.ucsf.edu/chimera/data/downloads/1.8/docs/UsersGuide/midas/v… From the help here it says: > (...) and inner and outer radii *r1* and *r2* (defaults are 90% of the > smallest radius and 110% of the largest radius of the displayed isosurface, > respectively, given the cylinder center and axis direction). Since this is a high-resolution cryo-EM map with many intricate features, it's hard to visually find exactly what are the smallest and largest radii currently displayed at the isosurface. So we'd like to know what ChimeraX is finding by itself and compare it to our measurements. Any tips are appreciated. Thank you! -- Ricardo Diogo Righetto

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Glb files
by Rowe-Magnus, Dean 28 Apr '24

28 Apr '24

Hello, Can you please tell me how to save a .glb file as a .pdb so that I can use Matchmaker to align the structures? Thank you, Dean

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How to show van der Waals surface
by 我就要柠乐 26 Apr '24

26 Apr '24

Dear Sir/Madam         Recently, I have been using ChimeraX for graphical analysis, and I find the software to be very user-friendly and efficient. I am currently facing a challenge where I want to display the van der Waals surface of a residue, similar to this illustration（https://doi.org/10.1038/s41467-022-31526-7）. However, I am not quite sure how to write the command correctly. I have looked up the commands on the official website and tried using these two:surface #1:230； surface style mesh. The bottom is open （the rad circle）, but I would like to have a complete van der Waals surface with closed openings, similar to what is typically seen in the literature. I would appreciate your assistance. Thank you！                                                                                                                       yours  sincerely                                                                                                                       yiwen 我就要柠乐 790639436(a)qq.com  

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