- ChimeraX-users - RBVI Mailing Lists

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

4 5

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.

3 2

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

1 0

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.

3 8

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

2 2

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

1 1

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

2 2

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/

2 1

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

13 May '25

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: > On May 13, 2025, at 6:08 PM, Yaowang Li <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: chimerax-users-bounces+liyaowang2911=163.com(a)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: liyaowang2911(a)163.com > Cc: 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 > > 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 <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@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 >> -- >> ben(a)salilab.org <mailto:ben@salilab.org> https://salilab.org/~ben/ >> "It is a capital mistake to theorize before one has data." >> - Sir Arthur Conan Doyle >> >> _______________________________________________ >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>

1 0

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

13 May '25

Dear all, I am trying to analyze the structures that were deposited in the https://pdb-ihm.org Such as the entry: 8zza The chimeraX (version 1.7 to 1.10) cannot read the CIF file with warning information warning No mmCIF models found. While it succeeded in opening it after adding the option format ihm. But they are the start model, restraints, and results, which is a coarse-grained model, instead of a real structural model consisting of atom coordinates. Could anyone help me figure it out? Best wishes

3 2

Re: Samsung 27" Odyssey 3D G90XF 4K 165Hz Monitor
by Tom Goddard 12 May '25

12 May '25

Hi Gökhan, The Samsung web page you referenced says the monitor is $3000, the same price as the Acer 27", and the Samsung also uses eye-tracking so it will probably only work for one person. The Sony and Acer displays both use OpenXR and eye tracking. This is good and bad. The good part is as you move your head to the side you see the side of the rendered objects. The bad is that most 3D applications do not support OpenXR unless they are VR applications. In contrast the Samsung uses side-by-side video input. That allows it to work with any 3D application that supports that common 3D format. Here's a description on Reddit talking about side-by-side input with the Samsung. (Unfortunately the Samsung manual does not say much.) https://www.reddit.com/r/Monitors/comments/1k8wnqa/samsung_odyssey_3d_g90xf… The drawback of the Samsung approach is that the monitor has no way to tell the application (e.g. ChimeraX) that your head has moved to the side (that is what OpenXR does). So when you move your head to the side you just see the same view direction of the 3D object only skewed. It's not a disaster, you can rotate the molecule if you want to see it from the side. The Samsung manual says only Windows is supported since they include some crappy software that runs on your Windows machine. I'm not sure if it is needed to handle side-by-side input. I'd love to see the Samsung display. It uses a 4K panel like the Sony and Acer. Like those displays it must be using a lenticular grating to send some pixels to your left eye and some to your right eye so the actual resolution in 3D is more like HD (2K). Still that is pretty good. (With old technology LCD shutter glasses you would get full 4K resolution since the two eye images use all screen pixels and just alternate in time.) If I had one of these displays I think I could make ChimeraX render full-screen side-by-side. Since you can't drag the ChimeraX graphics into a separate window I would try to add code to create a separate window and render to it as an option. My lab does not have money to spare to buy such a display (NIH funding problems), so don't expect to work on this. Tom > On May 7, 2025, at 11:19 PM, <tolung.bio(a)gmail.com> <tolung.bio(a)gmail.com> wrote: > > Hi Tom, > > This Samsung is less than half the price (27” for 2K USD) compared to the SONY in the review. > > Let me know if you can score one of these to test/develop for :) > > Cheers, > > Gökhan > > > From: Tom Goddard <goddard(a)sonic.net> > Sent: Thursday, 8 May 2025 8:45 AM > To: tolung.bio(a)gmail.com > Cc: chimerax-users(a)cgl.ucsf.edu > Subject: Re: [chimerax-users] Samsung 27" Odyssey 3D G90XF 4K 165Hz Monitor > > Hi Gökhan, > > There is no ChimeraX capability to make the graphics pane full screen, so it will not work with a 3D display that wants full-screen side-by-side stereo format. The graphics pane is not a docked panel like the other ChimeraX tools. The ChimeraX main window is a Qt QMainWindow which treats that center area specially and it cannot be detached into a floating window. I'm not sure how hard it would be to allow that. > > We are also working on glasses-free eye-tracked 3D displays such as the Sony Spatial Reality and Acer SpatialLabs displays. They use OpenXR and only work on Windows and only with 1 person viewing, and costly $3000-5000, so they have some limitations. Here's a description of trying the Sony 3D display with ChimeraX > > https://www.rbvi.ucsf.edu/chimerax/data/sony3d-mar2025/sony3d.html > > Tom > > > >> On May 7, 2025, at 12:24 AM, Gokhan via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote: >> >> Hello ChimeraX team and users, >> >> Does ChimeraX support this monitor? >> >> https://www.samsung.com/au/monitors/gaming/odyssey-3d-g90xf-27-inch-165hz-u… >> >> I read a very positive review about this monitor and may consider buying one if it works with ChimeraX. >> >> The review says that this monitor needs a full-screen side-by-side output. Just as many of the sub-windows of ChimeraX can be docked and undocked (e.g., log, Models, etc.), is there way to ‘undock’ the main graphics window to make it full screen? Or, is there a way to display the graphics window on a secondary monitor as a full-screen output? >> >> Thanks, >> >> Gökhan >> >> _______________________________________________ >> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> >> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu <mailto:chimerax-users-leave@cgl.ucsf.edu> >> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/

3 10

Samsung 27" Odyssey 3D G90XF 4K 165Hz Monitor
by tolung.bio＠gmail.com 07 May '25

07 May '25

Hello ChimeraX team and users, Does ChimeraX support this monitor? https://www.samsung.com/au/monitors/gaming/odyssey-3d-g90xf-27-inch-165hz-uh d-ls27fg900xexxy/?srsltid=AfmBOopLIkVAywsvNylPGVRL3wUoUJuBvUOPOz0metBjwLM2Nn xgmQVf I read a very positive review about this monitor and may consider buying one if it works with ChimeraX. The review says that this monitor needs a full-screen side-by-side output. Just as many of the sub-windows of ChimeraX can be docked and undocked (e.g., log, Models, etc.), is there way to undock the main graphics window to make it full screen? Or, is there a way to display the graphics window on a secondary monitor as a full-screen output? Thanks, Gökhan

2 1

including HET atoms in kvfinder calculations from ChimeraX
by Elaine Meng 07 May '25

07 May '25

> On May 7, 2025, at 2:01 AM, Mühleip, Alexander <alexander.muhleip(a)helsinki.fi> wrote: > > Hi Elaine, > > I am checking out the new kvfinder tool in ChimeraX. I was wondering if there is some way to prevent it from disregarding heteroatoms in the cavity search (in my eyes, e.g. excluding hemes is not helpful). I tried changing the selection syntax, but I think the pruning is taking place internally in kvfinder. > > Is there some way to interfere with it or make an ignore option (like the isolde implementation in chimerax has)? > > Best wishes, > Alex > > Alexander Mühleip > group leader > HiLIFE-Institute of Biotechnology > University of Helsinki > Finland > +358503282167 Hi Alex, Generally it's better to ask on the chimerax-users list, since as the resident non-programmer I often don't know implementation details. I CC'd the list in case others may also be interested in this topic. After consultation with the programmer who implemented this tool, we could not think of any current workaround. It uses the "main" category of atoms (definition in link below) which is automatically assigned cannot be manually overwritten. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#surfcats> However, we can consider this a request for enhancement that might be added in the future. Best wishes, 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

1 0

Options to align two models and calculate per-residue RMSD
by christian.steinmetzger＠imbim.uu.se 07 May '25

07 May '25

Dear ChimeraX users, I'm working with some different ribosome structures which I first want to align to a reference structure (as rigid bodies) and then calculate RMSD values with respect to the reference. The number of chains are the same between my structures and the reference, and the chain names + residue numbers are congruent as well. However, some of my chains have residues missing or added at the ends, have a small number of insertions (using insertion codes in the pdb file) or point mutations. What I have tried so far is: "matchmaker #2 to #1 pairing ss show true" "save file.defattr #2 attrName r:seq_rmsd modelIds false" (to store the resulting RMSD values for later use) which aligns based on CA for protein chains and C4' for RNA. I haven't given any explicit chain specification (each model has 56 chains). Am I correct to think that the RMSD values I get are based on a whole-structure rigid-body alignment that takes all chains into account simultaneously? Or does it align each chain in #2 to its matching chain in #1 individually? For the proteins I think per-residue CA-RMSD values are suitable for what I need, but for the RNA chains I would like to get per-residue all-atom RMSDs, not just C4'. Can this be achieved with matchmaker? I have also tried to use the align command like this: "align #2 toAtoms #1 each structure matchChainIds true matchNumbering true" which, to my understanding, would do the alignment not just based on CA/C4', but for all atoms. Is that correct? With this, what would be the best way to extract per-residue RMSD values? The "rmsd" command rightfully complains about unequal numbers of atoms between #1 and #2. Is there a way to implicitly select only the atoms that are congruent between #1 and #2? Kind regards, Christian

2 2

RMSD for all frames in a trajectory
by Alexandra Zahradnikova 07 May '25

07 May '25

Dear All, I am working with a trajectory of a tetramer. I would like to align the A chains in all frame of the trajectory and then calculate the rmsd of all chains in all frames relative to the respective chain of the first frame (i.e., align only chains A but calculate for all chains), and write the results to a text file. Is that possible? I can do a similar calculation with a script in old Chimera but don’t know how to do it in ChimeraX. I attach the zipped script for old Chimera. Best regards Sasha

2 6

Re: [Chimera-users] Add sequence logo to view
by Elaine Meng 05 May '25

05 May '25

Hi Alex, Sorry no we do not have a feature like that currently. (P.S. It may be better to use the chimerax-users(a)cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu> address CC'd here for ChimeraX questions.) In ChimeraX: The most similar thing I can thihk of is that for deep mutational scanning results it is possible to show labels with the scores of each residue type shown in a color-coded grid, but the "rub" is that you would have to open the data from a specific format we are using for these kinds of results: mutation scores format: <https://rbvi.ucsf.edu/chimerax/docs/user/formats/mutationcsv.html> I could imagine that instead the sequence alignment profile at each position could be shown as a similar label. ChimeraX has a new profile-grid viewer for sequence alignments as an optional alternative to the standard viewer, <https://rbvi.ucsf.edu/chimerax/docs/user/tools/profilegrid.html> .... so such a label could essentially be the profile column rearranged into a squarish grid, as in the mutational scanning labels image above. However, that has not yet been discussed (nor implemented, of course). We do not have any sequence logo type of display. 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 > On May 5, 2025, at 7:35 AM, Alexander Lee via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear ChimeraX community, > > I have a consensus sequence + logo done in an outside program. Is there a way to superimpose this onto a crystal structure? When hovering my mouse over a residue in the structure viewer (or sequence viewer), I would like the logo to come up. Is there a similar feature available? > > Regards, > Alex > _______________________________________________ > Chimera-users mailing list -- chimera-users(a)cgl.ucsf.edu > To unsubscribe send an email to chimera-users-leave(a)cgl.ucsf.edu > Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/

1 0

How can I overlay the 2Fo-Fc density map onto the amino acid residues I specified?
by 1025049892＠qq.com 04 May '25

04 May '25

Every time I open the map file in ChimeraX, I find that it doesn't overlap with my PDB structure. Why is this the case, and how can I make them match? Thank you for your attention. I'm looking forward to your reply.

4 5

Morphing of structures with different chain numbers
by Enrico Martinez 01 May '25

01 May '25

Dear ChimeraX Users, I am trying to perform a morphing between two cryo-EM structures of the same complex, where one structure has twice the number of chains as the other (PDBs 3J9K and 8Y6Q). However, the larger structure causes an error during morphing. I have attempted to write a script that aligns the two structures and deletes the unmatched chains from the larger structure. Unfortunately, the script is not working as expected. from chimerax.core.commands import run def delete_unmatched_chains(session): # Get models #1 and #2 m1 = next((m for m in session.models if m.id == (1,)), None) m2 = next((m for m in session.models if m.id == (2,)), None) if m1 is None or m2 is None: session.logger.info("Model #1 or #2 not found.") return chains1 = {chain.chain_id for chain in m1.chains} chains2 = {chain.chain_id for chain in m2.chains} unmatched = chains1 - chains2 if unmatched: chain_ids = ",".join(unmatched) # Deleting unmatched chains run(session, f"delete /{chain_ids}") session.logger.info(f"Deleted chains: {', '.join(unmatched)}") else: session.logger.info("No unmatched chains found.") Could you please help me or alternatively propose another solution? Any suggestions would be greatly appreciated. Thank you in advance ! Enrico

3 6

Saving Images with Specific Dimensions and DPI in ChimeraX
by svle＠tiscali.it 30 Apr '25

30 Apr '25

Hi, In Chimera, when saving an image, it's possible to specify the output size in centimeters and the resolution in DPI. This feature is very useful for preparing figures for theses and publications. Is it possible to do the same in ChimeraX? I've read the documentation for the save command, but it's not entirely clear to me how to achieve this. Do you have any suggestions? Best regards, Saverio

2 3

Reproducing the Chimera Preset Publication 5 ( flat ribbon ) in ChimeraX
by svle＠tiscali.it 29 Apr '25

29 Apr '25

Hi, it is possible to reproduce the Chimera Preset Publication 5 ( flat ribbon ) in ChimeraX? What are the commands to use in order to have this type of preset in ChimeraX? This is a very nice preset. Thanks. Saverio

2 2

How to apply symmetry I to generate an icosahedron model
by 唐延婷 29 Apr '25

29 Apr '25

Hi doctor, when I open a map (ID 1) and a model (ID 2), the map is the whole icosahedron while the model is the protomer of the icosahedron. I want to apply symmetry I to generate an icosahedron model. I have rotated and translated the model into a reasonable position inside the map and then done a “fit in map” to get the initial placement for sym. Then I enter a command ''measure center #1''，center of mass xyz coordinates for map_sharp.mrc = (238.08, 238.08, 238.08)，enter another command ''sym #2 I,222 center 238.08, 238.08, 238.08'' I can see an icosahedron model fit in map. But when I save the icosahedron model.pdb, I found the icosahedron model actually is the model of the protomer. How can I apply symmetry I to generate a true icosahedron model, used for subsequent model refine in coot and real_space_refine in Phenix. Thank you very much. Best wishes! yanting 延婷 yanting.tang(a)mail.nankai.edu.cn

2 2

Issues with find cavities tool
by Marino, Claudia 28 Apr '25

28 Apr '25

Greetings, I am not sure why I recently cannot longer use the tool “find cavities”. My ChimeraX version is 1.9 and my MacOS is Sequoia 15.4. Please, find below the screenshot of the Error message. [cid:image001.png@01DBA7F0.57B85750] Thank you very much in advance for your help. Sincerely, Claudia.

3 11

reduce gridpoints on the cryoEM map (640 x 640 x 640 ) to ( 320 x 320 x 320)
by arangarajan＠initialtx.com 28 Apr '25

28 Apr '25

hi, i need to reduce the grid points to make the map work with MOE. I am not sure if this is possible in chimerax and i would appreciate some suggestions for creating a mrc file with reduced grid points. please let me know your thoughts. best amith

2 2

VR on ubuntu workstation
by arangarajan＠initialtx.com 24 Apr '25

24 Apr '25

Hi, i got steam VR installed but later found out that Oculus does not support linux. Is there a work around for using chimerax VR on latest ubuntu machine with oculus rift s headset? i can get other headset also if it will fit this purpose. thanks in advance, best amith

2 3

Effect of clearing ChimeraX cache from Mac?
by Radford, Katelyn M. (Kate) 23 Apr '25

23 Apr '25

Hi there! I'm in the throes of a memory-expensive project and my computer is running out of space. A little bit of googling led me to conclude that it would probably make sense for me to clear my system's cache, as my system files take up about a third of my disk space. ChimeraX cache files account for a substantial portion of that memory usage. As I make figures, I save .cxs files of each figure so that it's easy to go back and edit things that need to be changed. My ChimeraX also has a bunch of plug-ins installed (e.g. ISOLDE). I'm wondering: how much damage will I do to my installation and to my .cxs files if I delete the ChimeraX cache? System and software details: ChimeraX version: 1.9 MacOS: Ventura 13.0 Chip: Apple M2 Max Thank you all so much for the excellent work you do, Best wishes, Kate Kate Radford (she/they) PhD candidate, Biochemistry and Molecular Biophysics California Institute of Technology 1200 E California Blvd Pasadena, CA 91125

3 2