- ChimeraX-users - RBVI Mailing Lists

Re: [Chimera-users] Finding SASA for individual residues
by Elaine Meng 29 Aug '24

29 Aug '24

Hi Ale, In the future please use chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> (CC'd here) for ChimeraX questions. This chimera-users@cgl address is for Chimera, which is a different program, and I don't want to confuse the other users. Everybody, this answer is for ChimeraX: I believe you are misunderstanding how "measure sasa" works. It will actually enclose the specified atoms in a surface, so if you say "measure sasa :12" that surface will only be around residue 12 and ignore all the other atoms. I am guessing that you really want the SASA of the aromatic rings in the context of the surface that goes around the whole protein, not for a bunch of individual bubbles drawn around each aromatic ring. In that case, your commands are wrong. Instead you want something like: measure sasa protein sum :trp,tyr,phe & aromatic-ring See "measure sasa" help for description of how it works: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/measure.html#sasa> 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 > On Aug 29, 2024, at 4:16 AM, alessandro.strofaldi--- via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > > I'll reply to this post for my question cause the title seems appropriate. > I've a one-chain protein and I simply want to calculate the SASA of the aromatic-ring of all TRP,TYR and PHE of the protein using ChimeraX. > > This is the log: > measure sasa /A > Solvent accessible area for /A = 22276 > measure sasa /A:trp & aromatic-ring > Solvent accessible area for /A:trp & aromatic-ring = 1824.9 > measure sasa /A:phe & aromatic-ring > Solvent accessible area for /A:phe & aromatic-ring = 3339.6 > measure sasa /A:tyr & aromatic-ring > Solvent accessible area for /A:tyr & aromatic-ring = 3977.3 > > But the I tried to get the sum: > > measure sasa /A:trp,tyr,phe & aromatic-ring sum :trp,tyr,phe > Solvent accessible area for /A:trp,tyr,phe & aromatic-ring = 7683.3 > Solvent accessible area for :trp,tyr,phe (285 atoms) of /A:trp,tyr,phe & aromatic-ring = 7683.3 > > Which is different from the sum of the values I got before. I think I'm missing something basic on SASA calculations... > Also, from your answer to Prathvi, those numbers should be squared Agstrom. Do these number make sense? For a single residue (measure sasa:263, which is a surface-exposed Tyrosine) I got 331.95. Those values are similar to what Prathvi got so am I doing the same mistake? I was expecting, for a single residue something like two order of magnitude less. > You said ".. then it will make a surface that only encloses that one residue, with area 292 as you said. I'm pretty sure that is NOT what you want. Instead you want tthe surface of the whole protein (or maybe one chain) and then the area of the residue given that larger surface. " Does this means that with the commands I typed ChimeraX "Isolates" the residue and calculate the SASA as if it was not included in the protein? > Anyway, I think it is clear I'm an unexpert user so If there is any tutorial about SASA on ChimeraX (could not find those, only for Chimera), please, feel free to suggest. > > Thank you!! > Best, > Ale

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Re: Command line interface saving
by Mark Rosenberg 26 Aug '24

26 Aug '24

Thanks, Guillaume, for the excellent service. I found the log window now. I cannot cycle through my previous commands, though; in the bottom window, “command:’ with the down and up arrow. Is there a way to import those, please? Many thanks Mark mjfssmr mark.rosenberg(a)manchester.ac.uk<mailto:mark.rosenberg@manchester.ac.uk> mjfssmr mark.rosenberg(a)manchester.ac.uk<mailto:mark.rosenberg@manchester.ac.uk>mjfssmr mark.rosenberg(a)manchester.ac.uk On 26 Aug 2024, at 12:46, mjfssmr <http://mark.rosenberg@manchester.ac.uk> wrote: Thanks, Guillaume, for the excellent service. I found the log window now. I cannot cycle through my previous commands, though; in the bottom window, “command:’ with the down and up arrow. Is there a way to import those, please? Many thanks Mark mjfssmr mark.rosenberg(a)manchester.ac.uk mjfssmr mark.rosenberg(a)manchester.ac.uk On 26 Aug 2024, at 12:31, Guillaume Gaullier <http://guillaume.gaullier@KEMI.UU.SE> wrote: Hello, The log of your saved session should be there, but it is hidden at the top of the log window when you re-open the session file. There should be a black triangle that you can click to open the log contents from the previous session. I hope this helps, Guillaume ________________________________ From: Mark Rosenberg via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Sent: Monday, August 26, 2024 1:26:25 PM To: chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Command line interface saving Hi If I save my session in .cxs format, move to another machine, and open the same session again, I “lose" my commands. The commands don’t appear to be saved. How do I remedy this, please? Thanks Mark VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. 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/ [http://uu.se<https://urldefense.com/v3/__http://www.uu.se/om-uu/dataskydd-personuppgifte…> 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 [http://uu.se<https://urldefense.com/v3/__http://www.uu.se/en/about-uu/data-protection-po…>

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Re: Command line interface saving
by Guillaume Gaullier 26 Aug '24

26 Aug '24

Not that I know, sorry. But maybe somebody else knows, so it is better to keep the list in CC. 😊 Cheers, Guillaume ________________________________ From: Mark Rosenberg <mark.rosenberg(a)manchester.ac.uk> Sent: Monday, August 26, 2024 1:46:29 PM To: Guillaume Gaullier Subject: Re: Command line interface saving Thanks, Guillaume, for the excellent service. I found the log window now. I cannot cycle through my previous commands, though; in the bottom window, “command:’ with the down and up arrow. Is there a way to import those, please? Many thanks Mark mjfssmr mark.rosenberg(a)manchester.ac.uk mjfssmr mark.rosenberg(a)manchester.ac.uk On 26 Aug 2024, at 12:31, Guillaume Gaullier <guillaume.gaullier(a)KEMI.UU.SE> wrote: Hello, The log of your saved session should be there, but it is hidden at the top of the log window when you re-open the session file. There should be a black triangle that you can click to open the log contents from the previous session. I hope this helps, Guillaume ________________________________ From: Mark Rosenberg via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Sent: Monday, August 26, 2024 1:26:25 PM To: chimerax-users(a)cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Command line interface saving Hi If I save my session in .cxs format, move to another machine, and open the same session again, I “lose" my commands. The commands don’t appear to be saved. How do I remedy this, please? Thanks Mark VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. 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/ [uu.se]<https://urldefense.com/v3/__http://www.uu.se/om-uu/dataskydd-personuppgifte…> 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 [uu.se]<https://urldefense.com/v3/__http://www.uu.se/en/about-uu/data-protection-po…> VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe.

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Command line interface saving
by Mark Rosenberg 26 Aug '24

26 Aug '24

Hi If I save my session in .cxs format, move to another machine, and open the same session again, I “lose" my commands. The commands don’t appear to be saved. How do I remedy this, please? Thanks Mark

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molmap command question
by Grigory Mechetin, Ph.D. 23 Aug '24

23 Aug '24

Dear ChimeraX developers, when I use the molmap command on grid ('molmap #1 10 onGrid #2', grid2 was created with' vop new size 256,256,256 gridSpacing 0.74' command ) I get half-map. How to get the full one? When I use molmap without onGrid it generates the volume with non-equal grid size, but I need square 256^3 grid. [cid:3853c8fe-0ccd-4133-ba08-4732e3be8905] Best regards, Grigory Mechetin, PhD, MEMS, Duke University.

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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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Alligning a trajectory
by ygilron＠asu.edu 19 Aug '24

19 Aug '24

Hi I am new to UCSF ChimeraX, and would like to learn how to use it for visualizing trajectories. Previously, I was using pymol for this, but would like to use ChimeraX's better image rendering for a publication. I was able to load the .pdb file of my trajectory with: open <"path/to/pdb"> format pdb coord T Currently, this is the info of my file: >info 1 models #1, lambda25_trajectory_1k_res.pdb, shown 8094 atoms, 8219 bonds, 514 residues, 1 chains ( ), 100 coordsets I would like to remove translations and rotations by fitting each frame with a command similar to 'align': align matchatoms toAtoms refatoms [ cutoffDistance d ] [ move what ] [ each level ] [ reportMatrix true | false ] pairing-options Although, it seems I would have to do this manually 99 times for each pair of coordsets of the trajectory. Additionally, I am not sure I have the correct syntax for choosing a coordset from a model: align #1 , 1 toAtoms #1 ,2 gave me the following output: align #1 , 1 toAtoms #1 ,2RMSD between 8094 atom pairs is 0.000 angstroms That probably shouldn't be that accurate, right? In PyMOL one would use the command: intra_fit <model name> in order to do this. The best I was able to deduce was the following command: coordset #1 1,100 holdSteady @ca I am not sure if this is doing the same thing (rmsd fitting of model #1 coordset 1 to model #1 coordset 2.... ....model #1 coordset 99 to model #1 coordset 100 ) but rather just fixing the C-alpha atoms in place? is this equivalent? Also, I noticed this only aligns the coordsets once, and then reverts back to the default trajectory of tumbling around with all the rotations and translations. How can I set this holdSteady to be permanent for all future plays of my trajectory? Best, Yishai

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2D labels colored by chain color
by NG, Cheukhei Jackie [Student] 19 Aug '24

19 Aug '24

Dear sir/madam, I am trying to generate publication-quality images with chimeraX with appropriate 2D labels. 1. Is there a variable I could use to represent the coloring of my current chain so i can apply in the command where the selection is multiple chains: label sel color (the variable)? 2. is the an offset parameter or any relevant parameters in the 2D label command that are recommended for publication use? Thank you very much for your time. Thanks, Jackie [https://www.polyu.edu.hk/emaildisclaimer/PolyU_Email_Signature.jpg] Disclaimer: This message (including any attachments) contains confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this message and notify the sender and The Hong Kong Polytechnic University (the University) immediately. Any disclosure, copying, or distribution of this message, or the taking of any action based on it, is strictly prohibited and may be unlawful. The University specifically denies any responsibility for the accuracy or quality of information obtained through University E-mail Facilities. Any views and opinions expressed are only those of the author(s) and do not necessarily represent those of the University and the University accepts no liability whatsoever for any losses or damages incurred or caused to any party as a result of the use of such information.

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Feature of chimera
by Arpita Nandy 19 Aug '24

19 Aug '24

Hi, I am a PhD student from Germany and would like to make a figure where I can highlight specific proteins of interest in the mitoribosome complex of yeast. Could you please assist me to use ChimeraX in this context. Best regards Arpita Nandy

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Usage and Distribution of ChimeraX at our Upcoming Max Planck Institute Summer School
by SantaLucia, Daniel 15 Aug '24

15 Aug '24

Hello ChimeraX team, My name is Dan SantaLucia; I'm a research scientist working under Prof. Frank Neese and Prof. Serena DeBeer at the Max Planck Institute for Chemical Energy Conversion. One thing we do every year is to organize a summer school for students from all over the world, where they get to learn in-depth about many different spectroscopic techniques as well as quantum chemical calculations to help them in their interpretations of these datasets. You can find more information here, if you're curious: https://summerschool.cec.mpg.de/en/home thing that would be really nice would be to offer students the ability to use ChimeraX alongside our tutorial/practical sessions. We use ORCA to do calculations (considering, of course, that Frank invented it), and we've found that ChimeraX has a lot of really nice features that would be perfect for helping the students to learn. What I wanted to ask was this: do we have permission to distribute the download files at: https://www.rbvi.ucsf.edu/chimerax/download.html to the students? They would be distributed on flash drives that we give to the students, and we would distribute the Windows, Mac, and Linux versions so that we could cover all users. The internet connection is not the best, unfortunately, at our venue, which is why they can't just go to the link to download it themselves. To be clear: this is a non-commercial use event, where we simply have international students coming to attend the summer school, and this is an event that is for learning purposes only. Nonetheless, I want to have your explicit permission for distribution of ChimeraX to the students as well as your permission for them to use your software at our summer school? Thanks so much, and looking forward to hearing back from you, -Dan [1668779311055] [1668779979115] Dr. Daniel J. SantaLucia MPI-KoFo/CEC Joint Workspace Stiftstraße 34-36 45470 Mülheim an der Ruhr Germany Tel.: +49 208 306 3724

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problem to open a swiss dock results file
by Aurélie Hoeffel 13 Aug '24

13 Aug '24

Dear Chimeras members, I would be interested to use chimera x for interpreting some results of my docking. I precise it is the first time I use swiss dock as well as chimera x, after receiving the swiss dock file in a tar.gz format, I compress it via 7Zip but then chimera x, is not able to process and open my document, ii is just written, tar data ,Unrecognized file suffix '.tar', so I do not kwo if the pb come from chimera or swiss dock, do you know how I can solve the problem? Thanks in advance, Aurelie

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ChimeraX-daily (1.9, 5 Aug 2024); Log panel stealing focus
by leeyang+chimerax＠gmail.com 10 Aug '24

10 Aug '24

Hi, Downloaded the above Daily (macOS 14.5, Universal), primarily for the workaround retrieving mmCIFs containing an underscore (#15557). I noticed that the Log toolpanel steals focus whenever it updates. Perhaps something that has already been dealt with? Otherwise, thought I should post it here. Cheers, Yang

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AlphaFold version in ChimeraX 1.8
by Anna Mestre Borras 09 Aug '24

09 Aug '24

Hi, I would like to confirm which is the AlphaFold version in ChimeraX 1.8 when using Tools --> structure prediction --> AlphaFold. Thanks! Best, Anna

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Could not display the lipid such as cardiolipin
by 杨雪梅 08 Aug '24

08 Aug '24

Dear ChimeraX support group, When I open my PDB with ChimeraX, some lipids (get from the coot library with three-code) could not be seen. When it open with pymol, the lipids were displayed normal. Have you met such problem and how did you fix it? Looking forward to your kind help. Sincerely yours, Xuemei Yang Chinese Academy of Sciences Shanghai Institute of Materia Medica

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Could not display the lipid such as cardiolipin
by Yang Xuemei 08 Aug '24

08 Aug '24

Dear ChimeraX support group, When I open my PDB with ChimeraX, some lipids (get from the coot library with three-code) could not be seen. When it open with pymol, the lipids were displayed normal. Have you met such problem and how did you fix it? Looking forward to your kind help. Sincerely yours, Xuemei Yang Fudan University Chinese Academy of Sciences Shanghai Institute of Materia Medica

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problem for the PDB deposition
by Yanhe Zhao 07 Aug '24

07 Aug '24

Dear ChimeraX community and developer, I am trying to deposit my map with model. I save the model from pdb to cif in ChimeraX because of large amount of atoms, then got error as "Missing '_entity_poly.pdbx_strand_id' item. I tired to use pymol to open my pdb and save it as cif by 'Export Molecule', in which I just use the default options. I checked the saved cif in ChimeraX, which is weird since it couldn't be show in cartoon style. Is there any easy to handle this in ChimeraX or any option should be used in the 'Export Molecule' in Pymol? Thanks and cheers, Yanhe

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