August 2024 - ChimeraX-users - RBVI Mailing Lists

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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