August 2024 - ChimeraX-users - RBVI Mailing Lists

Data handling / privacy policy information?
by Frumolt, Brian 23 Aug '24

23 Aug '24

Hi, We are looking at ChimeraX for commercial use. I was looking on the site for information related to data use and privacy policies. I understand the app runs locally, but was wondering whether it leverages any web services, or passes any data outside the local installation? We have strict data handling policies in place for our clients, so would need to be aware. If there is a policy document I missed, that would be ideal. Thanks! Brian This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying, or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please contact the sender immediately and permanently delete the original and any copies of this email and any attachments thereto.

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Morphing two GPCR conformations
by Enrico Martinez 23 Aug '24

23 Aug '24

Dear Chimera-X users! I try to use the morph command to model the conformational change of GPCR related to its activation. Having two superimposed conformations of the receptor, which are different in the position of the internal part of the transmembrane helix VI, I try to visualize the displacement of this helix using morph #2,1 frames 250 Unfortunately the produced trajectory looks very unnatural (one helix overlaps with another one). Would it be possible to improve the accuracy of such morphing e.g. providing some restraints? Many thanks in advance ! Enrico

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Mol 2.0 desktop version
by Nicholas Koylass 22 Aug '24

22 Aug '24

Good day, I am trying to interface ChimeraX with a XML file that was converted to json to perform MOLE Channel Coloring by Property. However, I did not use the mole server. I used the desktop version since the server was unavailable. Thus, I received this error : molepore-7sqf.json does not look like Mole Online json file, does not contain Channels. Can anyone assist me with this? Thanks, Respectfully, Nicholas Nicholas Koylass Ph.D. Candidate, Department of Physiology, Qiu Lab XDBio Graduate Program Johns Hopkins School of Medicine nkoylas1(a)jh.edu

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Restoration of missing helical fragments of the structure
by Enrico Martinez 22 Aug '24

22 Aug '24

Dear Chimera-X users ! Suppose I have a pdb structure with a missed C-terminal fragment corresponding to the transmembrane helical part that should anchor the protein in the membrane. Is it possible to use some built-in utilities (modeller?) to predict this missing fragment based on the full length sequence of the entire construct? Many thanks in advance Enrico

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results swiss dock
by Aurélie Hoeffel 21 Aug '24

21 Aug '24

Dear Chimeras members, I obtained some docking results from swiss dock, unfortunately my result.dock4 document is not readable in chimerax, I did not achieve to open it. Is it something special I have to do? Because, on the website it is written that we can directly upload it and it will work but for me chimerax did not recognize my .dock4 document. What should I do? Thank for the answer, Aurelie Hoeffel

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ChimeraX docker arm64
by Daniel Diaz 20 Aug '24

20 Aug '24

We are unable to install chimerax in our ubuntu 22.04 docker image when running on arm64 architecture. We use it to add hydrogen atoms to our cif files for our protein ML data engineering pipelines. We are trying to scale our dataset generation pipeline to the new cluster on TACC (vista) which has arm64 chips. We are running it in a singularity container, which I create by converting my docker image, and I am unable to build the docker image using arm64. How do you recommend we proceed? Here is the error stack: $ apt-get update --fix-missing && apt-get install -y /dependencies/chimerax-daily.deb Hit:1 http://ports.ubuntu.com/ubuntu-ports jammy InRelease Hit:2 http://ports.ubuntu.com/ubuntu-ports jammy-updates InRelease Hit:3 http://ports.ubuntu.com/ubuntu-ports jammy-backports InRelease Hit:4 http://ports.ubuntu.com/ubuntu-ports jammy-security InRelease Reading package lists... Done Reading package lists... Done Building dependency tree... Done Reading state information... Done Note, selecting 'ucsf-chimerax-daily:amd64' instead of '/dependencies/chimerax-daily.deb' Some packages could not be installed. This may mean that you have requested an impossible situation or if you are using the unstable distribution that some required packages have not yet been created or been moved out of Incoming. The following information may help to resolve the situation: The following packages have unmet dependencies: ucsf-chimerax-daily:amd64 : Depends: libasound2:amd64 but it is not installable Depends: libatk1.0-0:amd64 but it is not installable Depends: libbz2-1.0:amd64 but it is not installable Depends: libc6:amd64 but it is not installable Depends: libcairo-gobject2:amd64 but it is not installable Depends: libcairo2:amd64 but it is not installable Depends: libcrypt1:amd64 but it is not installable Depends: libcups2:amd64 but it is not installable Depends: libdbus-1-3:amd64 but it is not installable Depends: libdrm2:amd64 but it is not installable Depends: libegl1:amd64 but it is not installable Depends: libexpat1:amd64 but it is not installable Depends: libffi7:amd64 but it is not installable Depends: libfftw3-single3:amd64 but it is not installable Depends: libfontconfig1:amd64 but it is not installable Depends: libfreetype6:amd64 but it is not installable Depends: libgcc-s1:amd64 but it is not installable Depends: libgdk-pixbuf2.0-0:amd64 but it is not installable Depends: libgfortran5:amd64 but it is not installable Depends: libgl1:amd64 but it is not installable Depends: libglib2.0-0:amd64 but it is not installable Depends: libglu1-mesa:amd64 but it is not installable Depends: libgstreamer-plugins-base1.0-0:amd64 but it is not installable Depends: libgstreamer1.0-0:amd64 but it is not installable Depends: libgtk-3-0:amd64 but it is not installable Depends: liblzma5:amd64 but it is not installable Depends: libncursesw6:amd64 but it is not installable Depends: libnspr4:amd64 but it is not installable Depends: libnss3:amd64 but it is not installable Depends: libopenjp2-7:amd64 but it is not installable Depends: libosmesa6:amd64 but it is not installable Depends: libpango-1.0-0:amd64 but it is not installable Depends: libpangocairo-1.0-0:amd64 but it is not installable Depends: libpulse-mainloop-glib0:amd64 but it is not installable Depends: libpulse0:amd64 but it is not installable Depends: libsqlite3-0:amd64 but it is not installable Depends: libssl3:amd64 but it is not installable Depends: libstdc++6:amd64 but it is not installable Depends: libtinfo6:amd64 but it is not installable Depends: libuuid1:amd64 but it is not installable Depends: libwayland-client0:amd64 but it is not installable Depends: libwayland-cursor0:amd64 but it is not installable Depends: libwayland-egl1:amd64 but it is not installable Depends: libwayland-server0:amd64 but it is not installable Depends: libx11-6:amd64 but it is not installable Depends: libx11-xcb1:amd64 but it is not installable Depends: libxcb-glx0:amd64 but it is not installable Depends: libxcb-icccm4:amd64 but it is not installable Depends: libxcb-image0:amd64 but it is not installable Depends: libxcb-keysyms1:amd64 but it is not installable Depends: libxcb-render-util0:amd64 but it is not installable Depends: libxcb-util1:amd64 but it is not installable Depends: libxcb-xinerama0:amd64 but it is not installable Depends: libxcb1:amd64 but it is not installable Depends: libxcomposite1:amd64 but it is not installable Depends: libxcursor1:amd64 but it is not installable Depends: libxdamage1:amd64 but it is not installable Depends: libxext6:amd64 but it is not installable Depends: libxfixes3:amd64 but it is not installable Depends: libxi6:amd64 but it is not installable Depends: libxkbcommon0:amd64 but it is not installable Depends: libxkbcommon-x11-0:amd64 but it is not installable Depends: libxrender1:amd64 but it is not installable Depends: libxtst6:amd64 but it is not installable Depends: zlib1g:amd64 but it is not installable E: Unable to correct problems, you have held broken packages. -- Danny Diaz, PhD Deep Proteins @ IFML Department of Computer Science University of Texas at Austin

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Protein backbone representation
by Alex Henley 20 Aug '24

20 Aug '24

I was wondering how I can achieve this structure representation. The papers I read cite Chimera, but I cannot figure it out. Any help is appreciated.

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Per-Model Lighting Options
by ygilron＠asu.edu 20 Aug '24

20 Aug '24

I am trying to render different parts of my model in different styles. This is done to emphasize changes in a ligand's force field between different simulations. I would like every part of my model to be rendered in "full", and only change the style for my ligand so it will appear either as "flat", with or without a "silhouettes" toggled on. Is there an option to do this? I would like to just render my custom residue "DIO" in the "flat" style. As you can see from the output it is part of chain 1: " ...Non-standard residues in dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 DIO — (DIO) ..." I tried to use the following command to separately render different parts of a chain: lighting model #1:DIO flat from the console: >lighting modell #1:DIO flat Expected a keyword while selecting DIO fro the select menu and then running : lighting flat changes the style on the whole image. P.S. full output command when I loaded the molecule: open .\dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb" format pdb coordsets true Summary of feedback from opening C:\Users\yis\Desktop\Wenwei Lab\article\first_draft_figs\dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb warnings Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV ... 1997 messages similar to the above omitted dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb title: PH06_elaxed_rank_001_alphafold2_translated_100_xyz.pdbqt in water t= 0.00000 step= 0 [more info...] Chain information for dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 Chain Description ? No description available Non-standard residues in dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb #1 DIO — (DIO) FE2 — (FE2) dt_100_dio_grp1_ph06_traj_comp_center_fit.pdb has 1001 coordinate sets

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Thanks Elaine, Tom, Eric and team
by Artie Kushner 20 Aug '24

20 Aug '24

Apologies for an off-topic message. I'd like to express my gratitude to Elaine Meng in particular and the rest of the RVBI team who are tirelessly killing it in the Users mailing list with questions. On top of the amazing software, I appreciate the consistency, informativeness and thoughtfulness of each individual response. I learn a lot about ChimeraX and the community by reading other people's questions and answers. Thanks and kind regards from BC and Manitoba, Canada Artem

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Assistance Required: Visualizing Complete Amino Acid Residue with Cartoon Transparency in ChimeraX
by Amandeep Sharma (P24BB0001) 19 Aug '24

19 Aug '24

Dear ChimeraX users, I am reaching out for assistance with visualizing amino acid residues in ChimeraX, particularly when part of the residue is embedded within a cartoon structure representation. I am aiming to achieve a visualization similar to what is possible in PyMOL, where the complete residue is visible even when it intersects with other structural elements and adjust the transparency of the cartoon representation so that the embedded atoms of the residue can be clearly seen. I am struggling to get the desired result. To provide context and illustrate the issue, I am enclosing images of the current visualization: - *Image 1:* Shows the current state where part of the residue is obscured by the cartoon structure. - *Image 2:* Demonstrates the desired outcome where the residue is fully visible, including the embedded atoms. I am looking for a solution that combines the aspects seen in the two attached images, allowing for clear visualization of the residue and improved transparency. Thank you very much for your assistance. I look forward to your guidance on how to achieve this in ChimeraX. Best regards, Amandeep -- Amandeep Sharma PhD Student (2024-25) Dept. of Bioscience & Bioengineering Indian Institute of Technology Jodhpur Karwar 342037, Rajasthan

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