- ChimeraX-users - RBVI Mailing Lists

Re: request your help about ChimeraX
by Elaine Meng 21 May '25

21 May '25

> On May 21, 2025, at 7:19 AM, Pietro Rizza <pietro.rizza(a)unical.it> wrote: > > Hi Dr Meng > Please you could help me, how do you save the data in CHIMERAX? > How can I save the energy of different poses? > Thanks in advance > Sincerely > Pietro > Hi Pietro, It is better to send questions to the chimerax-users(a)cgl.ucsf.edu address (CC'd here so you don't have to send it again), unless you are including private data. If you send only to me, it may not get answered. I removed your attachment in case it was private, but I see you are using ViewDockX. Of course, the energies and other descriptors of each pose are read from your original input file, so they are already "saved" there, but maybe you are trying to save as a spreadsheet format like CSV? It was not clear from your question. The ViewDockX "Save" button will just save another file that has all of the coordinates as well as the scores (like your original input file). There is no option to save a CSV file from the table, sorry. The only similar possibility is to convert the ViewDockX columns into a model attribute with this recipe <https://rbvi.github.io/chimerax-recipes/vdx_attrs/vdx_attrs.html> ... and then use the "save" command to save an attribute file <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#attributes> ... but in my opinion it would be MUCH easier just to process these values from your original input file (the one output by the docking program). You just can't do it with ChimeraX, sorry. 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

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Questions about alphafold interfaces output discrepancies
by Bruno Hay Mele 20 May '25

20 May '25

Hi! I am dabbling with the alphafold interfaces command, and I cannot make sense of the data. In my user case, the table synthesis produced by the command says: Models Confident pairs #Res1 #Res2 4 23 12 12 opening the best model produces these relevant lines in the log 200 atoms, 188 bonds, 24 residues, 1 model selected alphafold contacts last-opened & /A toAtoms last-opened & /B distance 4.0 maxPae 5.0 Found 14 residue or atom pairs within distance 4 with pae <= 5 in the csv, the same model has these relevant columns: distance, max_pae, num_res1, num_res2, num_interface_res1, 4, 5, 246, 246, 20, num_interface_res2, num_interface_res_pairs, num_confident_pairs, 20, 42, 23, interface_res_num1, interface_res_num2 12 values 12 values I am struggling a bit to reconcile all these numbers. The 24 residues selected by chimera after opening are not anywhere else. I suppose these are #Res1 + #Res2 of the synthesis (and interface_res_num1 + interface_res_num2 in the csv)? Both the log synthesis and the csv report 23 as number of confident pairs, but the log message after opening best model says 14 residues (I assume these are those within the distance/pae constraint?) Why Confident pairs is not #Res1 + #Res2? I am also a little bit puzzled by the csv where I read num_interface_res_pairs = 42 and num_interface_res1, num_interface_res2 20 ( I was expecting either 21,21 for num_interface_res or 40 for num_interface_res_pairs. I attach the prediction I was using for diagnosing the problem. cheers, -- Bruno Hay Mele, PhD 2D-20, Biology Dept., University of Naples Federico II https://github.com/bhym/ | +39 081 67 9118

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Smooth MD script vs morph movie
by Alexander Lee 19 May '25

19 May '25

Dear ChimeraX developers, I have been wondering about the pros/cons between the 2 methods to smoothen a trajectory. If I provide a pdb and an nc trajectory file, I can use the smooth_md python script. If the trajectory originally has 100 frames , there will still be 100 frames after using the script. If I exported my trajectory into separate pdb models and morph between each of them, with the default of 50 frames created between each trajectory frame, there will be 5,001 frames after using the command. While importing many pdb's and morphing them takes longer than importing a trajectory and smoothing it, are there any benefits to using either one over the other? I remember seeing some post-production artifacts in smooth_md python script method like the hydrogens of a lysine being in an odd geometry briefly throughout the smoothed trajectory and am unsure if morph command would do the same. Regards, Alex

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Foldseek
by Lynne Howell 15 May '25

15 May '25

Hi Is there an easy way to export the list of similar PDB structures, the % sequence ID, E-value etc that can be found using FOLDSEEK to an excel file. Thanks in advance L __________________________________________________________________________ P. Lynne Howell Canada Research Chair (2006-2020) Senior Scientist, Program in Molecular Medicine The Hospital for Sick Children Professor, Department of Biochemistry, University of Toronto Office and Mailing address: Room 20-9-715 Peter Gilgan Centre for Research and Learning (PGCRL) 686 Bay St. Toronto ON M5G 0A4 Phone: 416-813-5378 (Internal 305378) Web page: https://lab.research.sickkids.ca/howell/ ________________________________ This e-mail may contain confidential, personal and/or health information(information which may be subject to legal restrictions on use, retention and/or disclosure) for the sole use of the intended recipient. Any review or distribution by anyone other than the person for whom it was originally intended is strictly prohibited. If you have received this e-mail in error, please contact the sender and delete all copies.

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Issues with the 1.9 release on macOS
by Zach Pearson 15 May '25

15 May '25

Hello everyone, I just came across a bug report on our ticket tracker regarding a missing SciPy symbol in the 1.9 release. The basic problem is that scipy has two macOS arm64 wheels up, and one is targeting a higher MACOSX_DEPLOYMENT_TARGET than the other. I think pip ignores this environment variable when selecting packages, so without qualifying that we need the lower deployment target version, pip selects the higher one on our build machines. I fixed this issue a few weeks ago for the 1.10 daily builds, before release candidates went out, so neither of those versions are affected. If you have an ARM Mac and your macOS is less than 14, you should use a daily build or release candidate. You can check your version of macOS by clicking on the Apple logo in the top left, then clicking “About This Mac”. Because we are so close to the 1.10 release, we do not plan to make a 1.9.1 release at this time. Our website will be updated to reflect this information shortly, along with a BlueSky announcement. Thank you, — Zach

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Search in Command History
by Roden Deng Luo 15 May '25

15 May '25

Dear ChimeraX team, Not sure if there is one already, would be great to have a search box in the "Command History" window. Best, Roden -- This message and its contents, including attachments are intended solely for the original recipient. If you are not the intended recipient or have received this message in error, please notify me immediately and delete this message from your computer system. Any unauthorized use or distribution is prohibited. Please consider the environment before printing this email.

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Atoms on the other side of the box
by Alexandra Zahradnikova 15 May '25

15 May '25

Dear all, I am trying to minimize the volume of my Gromacs simulation box and therefore in some frames of the trajectory, the atoms appear on the other side of the box. Is there a way to correct this problem in ChimeraX or do I need to resolve it in Gromacs? Best Sasha

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Re: error with trying to open a saved chimera .cxs session
by arangarajan＠initialtx.com 14 May '25

14 May '25

i am trying to open a saved chimerax session saved with version 1.10.dev202504020144 (2025-04-02) using a newly installation of daily build dated 2022-12-30 and i am getting this error : unable to restore session : need to update bundle To restore session: update atomic bundle to ver 1.60.5 or newer ( have 1.43.4) please let me know how to fix this, thanks amith

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Creating a virtual atom n Chimerax
by svle＠tiscali.it 14 May '25

14 May '25

HI, I want to draw a pseudobond between a real atom and the centroid of six carbon atoms. How it is possible define a virtual or pseudo atom with the coordinates of the centroid as one of the ends of the psudobond? Thanks. Saverio

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Re: cif file from pdb-ihm, the integrative structure
by Yaowang Li 13 May '25

13 May '25

Agreed, but has information on proteins and AAs yaowang From: Tom Goddard <goddard(a)sonic.net> Sent: Wednesday, May 14, 2025 9:37 AM To: Yaowang Li <liyaowang2911(a)163.com> Subject: Re: [chimerax-users] cif file from pdb-ihm, the integrative structure Molstar is showing a tube through the beads of the coarse grain model. Tom On May 13, 2025, at 6:28 PM, Yaowang Li <liyaowang2911(a)163.com <mailto:liyaowang2911@163.com> > wrote: Hi Tom The chimerax indeed can open the file, and I succeeded in opening it yesterday, same as you showed. Although the molstar program displays the atomic model, it is hard to analyze. Yaowang <image001.png> From: Tom Goddard < <mailto:goddard@sonic.net> goddard(a)sonic.net> Sent: Wednesday, May 14, 2025 9:17 AM To: Yaowang Li < <mailto:liyaowang2911@163.com> liyaowang2911(a)163.com> Cc: Ben Webb < <mailto:ben@salilab.org> ben(a)salilab.org>; ChimeraX Users Help < <mailto:chimerax-users@cgl.ucsf.edu> chimerax-users(a)cgl.ucsf.edu> Subject: Re: [chimerax-users] cif file from pdb-ihm, the integrative structure Hi Yaowang, You can open the 8zza IHM model in ChimeraX using open 8zza from pdbdev If you get tomorrow's ChimeraX 1.10 release candidate or daily build you could also use open 8zza from pdbihm I just added the database name "pdbihm" because pdbdev was the development name of the IHM repository and is being phased out. As Ben said 8zza is a coarse grain model. Although you will see spheres in the model they do not represent individual atoms. The may represent whole residues or large subunits. Tom IHM 8zza shown in ChimeraX: <image003.jpg> On May 13, 2025, at 6:08 PM, Yaowang Li < <mailto:liyaowang2911@163.com> liyaowang2911(a)163.com> wrote: Hi, Ben and Tom Thank you for your help. “Real structural model” is not the right expression; I mean an atomic model. There should be an atomic model that was generated from the coarse-grained model, and the molstar program on the IHM website can display its atomic model. So it will be perfect that I can open it in Chimerax for viewing this complex structure. In short, I just want to get the atomic model, not the coarse-grained model. Best wishes, Yaowang From: <mailto:chimerax-users-bounces+liyaowang2911=163.com@cgl.ucsf.edu> chimerax-users-bounces+liyaowang2911=163.com(a)cgl.ucsf.edu < <mailto:chimerax-users-bounces+liyaowang2911=163.com@cgl.ucsf.edu> chimerax-users-bounces+liyaowang2911=163.com(a)cgl.ucsf.edu> On Behalf Of Tom Goddard via ChimeraX-users Sent: Wednesday, May 14, 2025 2:01 AM To: <mailto:liyaowang2911@163.com> liyaowang2911(a)163.com Cc: <mailto:chimerax-users@cgl.ucsf.edu> chimerax-users(a)cgl.ucsf.edu Subject: [chimerax-users] Re: cif file from pdb-ihm, the integrative structure Hi Yaowang, As Ben points out 8zza is an integrative hybrid model (IHM). Unfortunately the PDB gives ChimeraX a file with suffix ".cif" for 8zza that does not use the atomic model mmcif dictionary. ChimeraX would need to look at the contents of the file to decide that it is using the IHM dictionary. Currently ChimeraX identifies file types using the file suffix ".cif". That is why it says "No mmCIF models found" when you open this file. I've made a ChimeraX bug report to see if we can improve this <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17661> https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/17661 ChimeraX is able to read the IHM files. So if you download the 8zza.cif file and open it in ChimeraX with "open ~/Downloads/8zza.cif format ihm" it will show you the coarse grain model. Tom On May 13, 2025, at 8:58 AM, Ben Webb via ChimeraX-users < <mailto:chimerax-users@cgl.ucsf.edu> chimerax-users(a)cgl.ucsf.edu> wrote: On 5/13/25 7:33 AM, Yaowang Li via ChimeraX-users wrote: I am trying to analyze the structures that were deposited in the <https://pdb-ihm.org/> https://pdb-ihm.org< <https://pdb-ihm.org/> https://pdb-ihm.org> Such as the entry: 8zza [...] which is a coarse-grained model, instead of a real structural model consisting of atom coordinates. Could anyone help me figure it out? 8zza is a model of the yeast nuclear pore complex. As you have observed, it is a coarse-grained model, not atomic. I'm not sure what you mean by "real structural model" but the resolution of the data in 2018 was such that only a coarse-grained structure was possible. That's what was deposited and that's what ChimeraX will show you. What are you trying to do? Ben -- <mailto:ben@salilab.org> ben(a)salilab.org <https://salilab.org/~ben/> https://salilab.org/~ben/ "It is a capital mistake to theorize before one has data." - Sir Arthur Conan Doyle _______________________________________________ ChimeraX-users mailing list -- <mailto:chimerax-users@cgl.ucsf.edu> chimerax-users(a)cgl.ucsf.edu To unsubscribe send an email to <mailto:chimerax-users-leave@cgl.ucsf.edu> chimerax-users-leave(a)cgl.ucsf.edu Archives: <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/> https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

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