- ChimeraX-users - RBVI Mailing Lists

Coloring according to the secondary structure
by Enrico Martinez 06 Jan '23

06 Jan '23

Dear ChimeraX users! I need to color cartoon representation of a protein according to its secondary structure (e.g. to color helix in red, b-stands in blue and coils in violet etc). I have already seen a built-in plugin in UCSF Chimera (but not in Chimera-X) that could do this job! Could you suggest commands that would be useful in Chimera-X? Many thanks in advance Cheers Enrico

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Unable to find the distance between centroid & any other atom in chimeraX
by Prathvi Singh 05 Jan '23

05 Jan '23

Hi Elaine, I declared the centroid of a tyrosine residue's ring by first selecting its ring members & then using the command: *define centroid sel radius 0.5* Next, when I try to find the distance between the centroid, I get an error whose screenshot I have attached with the email. The command that I am using to find the distance are: *dist sel* dist #1.1 #1.2 (here the distance is being calculated between two centroids) Please help - Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Unfocus in chimeraX using command line
by Prathvi Singh 05 Jan '23

05 Jan '23

Hi Elaine, Is there any equivalent of the "~focus" command in chimeraX? -- Prathvi Singh, Research Fellow, Department of Biological Sciences & Bioengineering, Indian Institute of Technology, Kanpur-208016

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Re: [chimerax-users] Remote control / Threading in ChimeraX
by Albert Smith-Penzel 05 Jan '23

05 Jan '23

Hi Tom, Thanks for the explanation. I’ll have to think and investigate a bit to see if my thread use is causing some problems elsewhere. Most of our code has been pretty stable, but there are still a few occasional glitches that I haven’t completely understood. Anyway, session.ui.thread_safe is perfect for resolving the issues we have with adding the surface to the empty session and running commands remotely. The curl solution also works; I had something like this implemented previously for some other purposes, but my own preference is to send commands/data directly rather than writing out a file to be read on the other end. Thanks again! Cheers, Albert ––––––––––––––––––––––––––––––––––– Albert Smith-Penzel, Ph.D. DFG Project Leader Institute for Medical Physics and Biophysics Leipzig University 04107 Leipzig, Germany E-mail: albert.smith-penzel(a)uni-leipzig.de <mailto:albert.smith-penzel@medizin.uni-leipzig.de> > On 4. Jan 2023, at 21:41, Tom Goddard <goddard(a)sonic.net> wrote: > > WARNUNG: Diese E-Mail kam von außerhalb der Organisation. Klicken Sie nicht auf Links oder öffnen Sie keine Anhänge, es sei denn, Sie kennen den Absender und wissen, dass der Inhalt sicher ist. > > WARNUNG: Diese E-Mail kam von außerhalb der Organisation. Klicken Sie nicht auf Links oder öffnen Sie keine Anhänge, es sei denn, Sie kennen den Absender und wissen, dass der Inhalt sicher ist. > > Hi Albert, > > ChimeraX is not designed to run arbitrary Python code multithreaded. There are many reasons. First the Qt window toolkit is not thread safe -- all Qt GUI calls have to be done in the main thread. Violating that often results in a crash. But even without the GUI, imagine the main thread is looping over the list of open models while a second thread decides to add a model to that list -- this could break the looping thread many ways. Python has a global interpreter lock which means it only can run one thread at a time. Still if you pause one thread and then change the state of the ChimeraX session in another thread, the first thread could throw errors in countless ways when it resumes at an arbitrary point in the code with the data structures changed. In general very little software is thread safe because it is very difficult to implement. Usually that is only done by making threads not modify any data structures used by other threads. > > Here are two solutions. 1) Have your listener thread run the Python code it receives in the main thread rather than the listener thread. There is a ChimeraX function that takes a function and queues it to be run in the main thread. > > session.ui.thread_safe(func, args...) > > Here is the code if you want to see how it works > > https://github.com/RBVI/ChimeraX/blob/2e33222fabb48edec76df6e82a10efedb54a8… > > A second solution is to use the ChimeraX remotecontrol communication for everything. That mechanism just runs ChimeraX commands, but you can run Python code using it by just sending the command "open script27.py" where you put the Python you want to run in a file script27.py. > > Tom > > >> On Jan 4, 2023, at 4:40 AM, Albert Smith-Penzel via ChimeraX-users <chimerax-users(a)cgl.ucsf.edu> wrote: >> >> Hello, >> >> I am working on a Python project that uses ChimeraX (currently running 1.5 to interactively view dynamics data by mapping it onto a molecule. All the figures/movies in this paper, https://www.nature.com/articles/s41467-021-27417-y <https://www.nature.com/articles/s41467-021-27417-y>, were made possible by Chimera! Also thanks to Tom Goddard for explaining to me how some of those figures could be made awhile ago (https://rbvi.github.io/chimerax-recipes/spherical_harmonics/spherical_harmo… <https://rbvi.github.io/chimerax-recipes/spherical_harmonics/spherical_harmo…> ). >> >> So we’re controlling ChimeraX remotely; we launch a session and then can send commands from Python over to Chimera and edit images from within our python code (while still allowing us to interact via the ChimeraX interface). The basic way this works is as follows >> >> launch chimeraX from our code, including a short python script >> python script imports our libraries, launches “cmxr” (chimeraX remote) >> cmxr uses multiprocessing.connection.Listener to listen for commands/data coming from Client in our python code >> !!!The Listener runs in a thread (threading.Thread) so that we continue to be able to interact normally with ChimeraX (launching the Listener without using a thread freezes ChimeraX while waiting for commands, rendering it unusable) >> Then, we just tell it to run some function(s) that we’ve imported into ChimeraX, and provide some data, atom ids, etc. over the Client/Listener connection >> >> There are a few things that I can’t figure how to make work via this process. We’ve had a few long-standing workarounds, but I’ve always been a little disturbed that we can’t get this all to work from python alone. At the moment, when we launch ChimeraX, we also enable remote control via curl, and some commands are then sent that way (remotecontrol rest start port XXXX) >> >> In particular, if I want to send commands that would normally be executed at ChimeraX’s command line, in principle I should be able to use chimerax.core.commands.run. If I execute “run” from a simple python script, everything works, but if I run it from within a thread (as required by our Listener setup), then ChimeraX freezes. So, we send these commands via curl on the remotecontrol instead. >> >> Second, is there a right way to open models/surfaces from the ChimeraX python shell? At the moment, we also open pdbs via curl commands. For pdbs, maybe I just don’t know the right python command. However, I am re-implementing spherical harmonics referenced above. Once I have prepared the surface (“s”), if I add it to session.models, it crashes chimeraX if it is being added within the listener thread, and if there are no models already open. If another model is already open, then it works just fine, and if I load the same modules/execute the same commands from within the python shell provided in ChimeraX, it also works (regardless of other models being open). It seems like maybe ChimeraX isn’t able to fully initialize the session from within a thread. >> >> I’ve grouped these problems together because I guess mainly they have to do with being unable to do some actions from within threads, and if there’s an explanation/workaround for dealing with that. >> >> Thanks for your help! >> >> Cheers, >> Albert >> >> >> >> ––––––––––––––––––––––––––––––––––– >> Albert Smith-Penzel, Ph.D. >> DFG Project Leader >> Institute for Medical Physics and Biophysics >> Leipzig University >> 04107 Leipzig, Germany >> E-mail: albert.smith-penzel(a)uni-leipzig.de <mailto:albert.smith-penzel@medizin.uni-leipzig.de> >> >> >> >> >> >> _______________________________________________ >> ChimeraX-users mailing list >> ChimeraX-users(a)cgl.ucsf.edu >> Manage subscription: >> https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users >

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Remote control / Threading in ChimeraX
by Albert Smith-Penzel 04 Jan '23

04 Jan '23

Hello, I am working on a Python project that uses ChimeraX (currently running 1.5 to interactively view dynamics data by mapping it onto a molecule. All the figures/movies in this paper, https://www.nature.com/articles/s41467-021-27417-y <https://www.nature.com/articles/s41467-021-27417-y>, were made possible by Chimera! Also thanks to Tom Goddard for explaining to me how some of those figures could be made awhile ago (https://rbvi.github.io/chimerax-recipes/spherical_harmonics/spherical_harmo… <https://rbvi.github.io/chimerax-recipes/spherical_harmonics/spherical_harmo…> ). So we’re controlling ChimeraX remotely; we launch a session and then can send commands from Python over to Chimera and edit images from within our python code (while still allowing us to interact via the ChimeraX interface). The basic way this works is as follows launch chimeraX from our code, including a short python script python script imports our libraries, launches “cmxr” (chimeraX remote) cmxr uses multiprocessing.connection.Listener to listen for commands/data coming from Client in our python code !!!The Listener runs in a thread (threading.Thread) so that we continue to be able to interact normally with ChimeraX (launching the Listener without using a thread freezes ChimeraX while waiting for commands, rendering it unusable) Then, we just tell it to run some function(s) that we’ve imported into ChimeraX, and provide some data, atom ids, etc. over the Client/Listener connection There are a few things that I can’t figure how to make work via this process. We’ve had a few long-standing workarounds, but I’ve always been a little disturbed that we can’t get this all to work from python alone. At the moment, when we launch ChimeraX, we also enable remote control via curl, and some commands are then sent that way (remotecontrol rest start port XXXX) In particular, if I want to send commands that would normally be executed at ChimeraX’s command line, in principle I should be able to use chimerax.core.commands.run. If I execute “run” from a simple python script, everything works, but if I run it from within a thread (as required by our Listener setup), then ChimeraX freezes. So, we send these commands via curl on the remotecontrol instead. Second, is there a right way to open models/surfaces from the ChimeraX python shell? At the moment, we also open pdbs via curl commands. For pdbs, maybe I just don’t know the right python command. However, I am re-implementing spherical harmonics referenced above. Once I have prepared the surface (“s”), if I add it to session.models, it crashes chimeraX if it is being added within the listener thread, and if there are no models already open. If another model is already open, then it works just fine, and if I load the same modules/execute the same commands from within the python shell provided in ChimeraX, it also works (regardless of other models being open). It seems like maybe ChimeraX isn’t able to fully initialize the session from within a thread. I’ve grouped these problems together because I guess mainly they have to do with being unable to do some actions from within threads, and if there’s an explanation/workaround for dealing with that. Thanks for your help! Cheers, Albert ––––––––––––––––––––––––––––––––––– Albert Smith-Penzel, Ph.D. DFG Project Leader Institute for Medical Physics and Biophysics Leipzig University 04107 Leipzig, Germany E-mail: albert.smith-penzel(a)uni-leipzig.de <mailto:albert.smith-penzel@medizin.uni-leipzig.de>

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How to get the average pTM scores from an Alphafold multimer prediction
by Chen, Henry 04 Jan '23

04 Jan '23

Dear Chimarax devs/users, I'm using ChimeraX Alphafold tool to do a multimer structure prediction. I was wondering how can I determine the average pTM score for each structure prediction? I get PAE.png and plddt.png file, but not a text file or anything that tells me the average pTM. (I was hoping the ranking file would give the average score but it does not) The models come with the pdb file as well as the scores.json files, but again I don't see anything that tells me the average pTM for the structure. Clearly the pTM per residue scores are saved in my pdb file, is there a command to average them all up? Thanks! Henry

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Capping termini ends
by Pranav Shah 04 Jan '23

04 Jan '23

Hi Team, Happy New Year! I look forward to all new developments you guys have in store for ChimeraX in 2023. Speaking of, is it possible to somehow display the ends of a protein termini with a spheres or something? I have certain view of my model in which the termini get partially obscured so it would be nice to prominently have them displayed in some manner... Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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Extracting the color name/hex code of a colored ribbon
by Theodora Bruun 23 Dec '22

23 Dec '22

Hello, I am just curious if there is a command for listing the current color name or hex code of an atom/ribbon that is colored in ChimeraX. For example, I open a previously colored structure and like the color of chain A and now I would like to use that same color and maybe apply to other chains in the structure. Is there a way other than just eye-balling it? Best, Theo

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using atomic coordinates to measure volume
by Harrison, Daniel P 23 Dec '22

23 Dec '22

Hello: I would like to calculate the maximum volume made by selection of atoms in a given structure. Can you provide guidance on how to go about this process? It seems like there should be a simple procedure in ChimeraX but I have failed to locate it. My specific problem: I would like to calculate the volume of the void created by ice under various conditions so that my physical chemistry students can quantify and visually understand partial molal volume non-ideality. I would greatly appreciate any assistance you can provide. Dan

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PDB upload TER card error
by HONG ZHAN 21 Dec '22

21 Dec '22

Dear all, I saved my protein coordinates in ChimeraX as pdb (it has multiple chains), however, when I was doing upload on the PDB, it shows this error, I am using ChimeraX 1.5rc202211091945 on Linux ubuntu 22.04 LTS. Coordinates issues: ERROR: There is no TER card at the end of polymer chain 'X'. All polymer chains should have a TER card at the end of each chain. Please add TER card and restart again. Many thanks! Hong

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phosphorylation
by Fabian Glaser 21 Dec '22

21 Dec '22

Dear experts, I would like to mutate a ser and a thr to phospo-serine and phospho-threonine, what is the easiest way to do it? Thanks a lot, fabian -------------------------- Fabian Glaser, PhD Structural and Computational Biology Unit The Lorry I. Lokey Center for Life Sciences and Engineering Technion - Israel Institute of Technology, Haifa, Israel

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ChimeraX linux binary problems
by Добромир Калчевски 19 Dec '22

19 Dec '22

Hello, I have installed Chimera linux from binary and everything was OK from the get-go. ChimeraX however, fails to start for library dependencies. As I understand the source depends on around 50 packages. I don't know (and I can find no indication on internet) how many libraries am I missing, but I'm also kind of limited in terms of disk space / linux size and my distro does not have a very nice package manager - Clear Linux (it installs entire bundles of similar packages, instead of single packages and once removed the disk size does not go down). Is it possible to make a ChimeraX linux binary which is as easy to run as the Chimera linux binary - universal for all distributions and including all necessary dependencies ? Best Regards, Dobromir

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ChimeraX linux binaries too inconvenient
by Добромир Калчевски 19 Dec '22

19 Dec '22

Hello, Can you provide ChimeraX linux binary as useful as the Chimera linux binary ? - without all of the dependencies being outside of the package. Also, can the package simply install in the /home/username/.local/CHIMERAX... directory, just as Chimera or in a similar path ? (makes uninstallation easy, saves disk space). Many distros do not have package managers as convenient as those of Red Hat or Debian. For example I use Clear Linux (for the performance) and the dependencies are not even in the package manager. There is also no explicit list of dependencies and according to your web site there are about 50 of them, anyway. Basically whatever I do there is always a missing library I cannot easily find / compile / have no time for it, etc., so ChimeraX for me is out of reach. I tried Chimera from the linux binary and it ran just fine, but it lacks something in the GUI, which ChimeraX does not. The visualization settings fields can be scrolled up and down, so if I load let's say 12 molecular orbitals - I can easily hide / show the ones I need, instead of having them all on the screen and using the "Data set list" to manually show / hide each one. Best Regards, Dobromir

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Re: [chimerax-users] color
by Elaine Meng 19 Dec '22

19 Dec '22

Hi Guan, To ensure you get an aswer, we recommend sending ChimeraX questions to chimerax-users(a)cgl.ucsf.edu (CC'd here). You can click the square "color well" for each model listed in the Model Panel to open your system color browser, which will show the code. See also this page for the names of the initial model colors... <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colortables.html> ...and then this page which shows the codes for the names <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html#builtin> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Dec 18, 2022, at 5:46 PM, Guan, Lan <Lan.Guan(a)ttuhsc.edu> wrote: > > Dear Elaine: > I like the color usage in chimeraX. I wonder if we could know the color code for the color auto-painted when we open it. > Thanks, > Lan

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Aligning atoms
by Noriega, Heather 18 Dec '22

18 Dec '22

Hello, I have a question about the alignment. Is there a way to get the glycans to align, one has a PEG docked to it and I was hoping to place the PEG and delete the glycan #2. I am unsure if it is possible. It gives me an error because the number of atoms are not equal. I attached the session. Thanks in advance. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega(a)bison.howard.edu 520-203-1883

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ChimeraX Alphafold Multiple jobs
by Rayees Mattoo 16 Dec '22

16 Dec '22

Hi, I was wondering if I could run multiple Alphafold jobs via ChimeraX using my Colab Pro. Also, very often Alphafold job submitted gets disconnected after some time (15 min or so) without completing the job, any solution to that? Best Rayees

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help please - electrostatic potential units and fit in map correlation
by Leslie Bridges 15 Dec '22

15 Dec '22

Dear All What are the units for electrostatic potential in ChimeraX? Is it possible to say whether the fit in map correlation represents a "good" fit for the atoms (e.g. if my correlations are above 0.75, can I conclude all the fits are good?) All the best, thanks Dr Leslie R Bridges Hon Snr Lecturer in Neuropathology St George's University of London

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no conformation comparison category in ChimeraX1.5 and ChimeraX-daily
by Jiang Xu 14 Dec '22

14 Dec '22

Hey Guys, I am new to ChimeraX and just trying to adapt from Pymol to ChimeraX. I am using a macbook pro (15-inch early 2018) running macOS Big Sur. I was trying to use the morph method of ChimeraX to record some clips for my publication. But I couldn't find the structure comparison tab from the tools dropdown list. I've tried the 1.5 and daily build version and I couldn't find this tab in both. Any suggestions? Thank you, Best, Jiang Xu

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Analysis of docking results
by Luigi Marongiu 14 Dec '22

14 Dec '22

Dear sir or madam, I am new to docking analysis. I obtained a model from SwissDock but there are some commands that do not work on ChimeraX. 1. I can load the molecule, which is composed by 4 homo-chains. I can select one chain (A); how can I delete or hide chains B-D. I can select chain A using select>chain`; is there a way to hide the others? 2. The model (saved in the file clusters.dock4.pdb) shows several ligands: [cid:c289e47f-ca49-4f27-9ad6-acef069f976e][cid:728d8f47-8cfb-445c-9476-ebb8a9d54ef9] Is there a way to show only the ligands with the highest docking score? 3. the tools>binding analysis>ViewDockX` says that "No suitable models found for ViewDockX". But is not this the "clusters.dock4.pdb"? How can I load the model into ChimeraX? Thank you. Best regards, Luigi Marongiu Ph.D., B.Sc. (Hons.)

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Morphing structures with ligands (glycans)
by Nebojsa Bogdanovic 13 Dec '22

13 Dec '22

Hello, I am looking into morphing several protein structures that contain glycans important form the function. The structures are all the same protein, in different states so the sequence info is good. Is there any function that retains the glycans visible once the command* morph #1-5 same true* produces a new model? I can just show them from origin structures but this does not look the best. Thank you and best regards Nebojša Bogdanović, Ph.D Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University

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Primer in chimeraX
by Luigi Marongiu 13 Dec '22

13 Dec '22

Dear sir/madam, I am new in the use of ChimeraX (for Linux). I would like to use ChimeraX for two jobs: 1. calculate the volume of a molecule (namley: maltose). I have uploaded the pdb of the molecule, selected the tools>volume>volume viewer, but I don't see any actual output. How can I get the value for the volume of this molecule? 2. show the docking of a ligand. I have obtained a docking model with swissdock, which I have loaded; how can I show the bonds between target and ligand? Thank you. Best regards, Luigi Marongiu Ph.D., B.Sc. (Hons.)

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Isolde loading issue
by Dmitry Semchonok 13 Dec '22

13 Dec '22

Dear colleagues, Is there any alternative for ISOLDE installation? >From ChimeraX 1.5 it doesn't load on my Mac - it stops. Kind regards, Dmitry

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using chimerx on unix
by Barak Yariv 11 Dec '22

11 Dec '22

Dear Chimera team, I'm from the ConSurf webservere https://consurf.tau.ac.il/consurf_index.php We have been working with chimera for many years and we want to update to chimerax. We have trouble installing chimerax on our unix system. We did manage to install it on our local computers in windows but when installing on unix we get an error: missing library PyQT6 Can you help us? Barak

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Specify unmodelled residues
by Jaremko, Matt Joseph 09 Dec '22

09 Dec '22

Hello ChimeraX Team, What information in the PDB file specifies the unmodelled residues (in black box)?: [cid:image001.png@01D90BDD.3983D7C0] I’d like to have this information in my own PDB files. Thank you, Matt Matt J. Jaremko, Ph.D. (He|Him) Senior Scientist | Protein & Structural Chemistry Merck Research Labs | 2000 Galloping Hill Rd. | Kenilworth, NJ 07033 Office: 908.740.5613 | Cell: 808.741.6277 | Email: matt.jaremko(a)merck.com<mailto:matt.jaremko@merck.com> This e-mail message, together with any attachments, contains information of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA 07065) and/or its affiliates, that may be confidential, proprietary copyrighted and/or legally privileged. (Direct contact information for affiliates is available at - Contact us - MSD<https://www.msd.com/contact-us/>.) It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system.

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Perframe and distance
by Simonson, Benjamin Thomas 09 Dec '22

09 Dec '22

Hello! I am trying to measure the distance between two atoms in my trajectory in every 10th frame. My approach was to use the perframe command paired with the distance command. Below was my attempt: perframe "distance /D:15@NH1 /B:42@OD1;distance save dist$1.txt;~distance /D:15@NH1 /B:42@OD1" interval 10 However, it instead simply outputs the distance of the currently displayed frame over and over again. Any help would be appreciated! Ben ......................................... Benjamin Simonson MCIBS PhD Candidate Penn State University

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How do I NOT "show disjoint surfaces"?
by Sungwook Woo 06 Dec '22

06 Dec '22

Hi I've been using UCSF Chimera and recently encountered ChimeraX -- I really like the modern look and feel! One feature I cannot find in the X version, though, is editing the attributes of an MSMS surface model, where I was able to disable (make 'false') the 'show disjoint surfaces' setting, in the original version. Most of the time dealing with models I don't need it, but sometimes I like to 3D print molecular models to really get a 'grip' on the models, and that feature of not showing disjoint surfaces has been useful to remove internal 'bubbles', which I learned about through this posting: https://www.cgl.ucsf.edu/pipermail/chimera-users/2009-May/003903.html . If internal bubbles are not removed, they waste printing material and increase printing time. Is there any way to disable showing disjoint surfaces, or otherwise achieve a similar goal in the X version? Thanks! Best, Sungwook

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swapna in ChimeraX
by Shahid, Taha (Dr.) 01 Dec '22

01 Dec '22

Hi all, Does ChimeraX have swapna functionality? I can find the swapaa command but not swapna. Is there another way to achieve its effects? If not, I think it would be useful addition. Kind regards, Taha

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ChimeraX 1.5 release not visible on website
by Shahid, Taha (Dr.) 01 Dec '22

01 Dec '22

Dear ChimeraX Team, I would like to update, but can't see either the ChimeraX 1.5 release candidate or production release on the USCF ChimeraX download page (only ChimeraX 1.4 and the daily build are available). Many thanks, Taha Dr Taha Shahid Postdoctoral Research Associate Leicester Institute of Structural and Chemical Biology Henry Wellcome Building | University Road | Leicester | LE1 7RH | UK e: ts387(a)leicester.ac.uk<mailto:XXXX@leicester.ac.uk> w: https://www2.le.ac.uk/institutes/liscb Follow us on Twitter<https://twitter.com/leicstructbio> [cid:D64185E6-9A9E-47F3-98A6-A33685D0B03A]

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chimerax freezing
by HOH Francois 30 Nov '22

30 Nov '22

Hi I had to change my hard drive and reinstall everything. When launching chimerax, it starts but freeze. Have to kill it. OS ubuntu 22.04. No special message in the log when using chimerax --debug Any idea ? Thank's FH ________________________________________ Hoh François, PhD Research Engineer Team BSME: Biologie structurale multi-échelles Centre de biochimie Structurale de Montpellier CNRS UMR 5048 - UM - INSERM U 1054 29 rue de Navacelles 34090 MONTPELLIER Cedex - FRANCE http://www.cbs.cnrs.fr Tel: (33) 04 67 41 77 29

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ChimeraX 1.5 release
by Elaine Meng 30 Nov '22

30 Nov '22

UCSF ChimeraX version 1.5 has been released! ChimeraX includes user documentation and is free for noncommercial use. Download for Windows, Linux, and MacOS from: https://www.rbvi.ucsf.edu/chimerax/ Updates since version 1.4 (Jun 2022) include: - AlphaFold search/fetch uses database v4 (fixes ~4% of v3 entries) - show AlphaFold residue-residue errors (PAE) with colored lines - Axes/Planes/Centroids tool to define objects, use in measurements - transform surface models (scale, shift, rotate) - add hydrogens GUI - calculate and assign charges, including for nonstandard residues - dock prep command - renumber residues, change chain IDs - crosseye and walleye stereo - cleaner close session (reverts more settings) - UniProt sequence fetch updated to work with UniProtKB's new API - DICOM browser shows patient-study-series hierarchy in medical image data For details, please see the ChimeraX change log: https://www.rbvi.ucsf.edu/trac/ChimeraX/wiki/ChangeLog

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Ribbon coloring
by F.Xavier Gomis-Rüth 30 Nov '22

30 Nov '22

Hi Elaine, when coloring a helix differently from the attached coils, is there a means to prevent the first short segment of the coil to get the color of the helix? It seems to me there was some kind of "halfbond"-mode one... Best, Xavier --

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Re: [chimerax-users] Placing a ligand in a protein structure from PDB
by Elaine Meng 30 Nov '22

30 Nov '22

> On Nov 30, 2022, at 7:41 AM, Amit Kugler <amit.kugler(a)kemi.uu.se> wrote: > > Hej Elaine, > > I found you on the ChimeraX website, and I have a question. > > I have a PDB file of my protein, but not showing a ligand. > > I am wondering if there a way I can add a ligand to the active site of the protein and write out the new PDB file on ChimeraX? > > Best regards, > Amit > Hi Amit, We recommend sending questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) to make it more likely you get a response. Not sure what you mean by add a ligand. Sure you can open a file of a ligand and open a file of the protein, and then combine them into one model, and then save. But probably you want to put the ligand in some sensible position, which could be done by moving it individually by hand, or by using some docking program. ChimeraX does not do docking. You would have to use some docking program (Glide, DOCK, Gold, Autodock, Autodock Vina, etc.) and then open the output from that docking program in ChimeraX. Moving models by hand, see this previous post: <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2017-November/000157.html> There is a "combine" command to combine the two separate models into a new single model, and "save" (or menu File... Save) to save the resulting combined model as a PDB file. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/combine.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> Or maybe you don't have a structure of the ligand. If there is some other PDB structure that contains it you can open that structure and delete all the rest of the atoms, or if you can find it in PubChem you can try fetching by PubChem ID into ChimeraX, e.g. command open pubchem:12120 <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#fetch> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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font size on the task bar
by Krishnan Raman 29 Nov '22

29 Nov '22

Is it possible to change the font size(larger) on the first line of the of the taskbar file…edit select etc… For viewing at from a distance on a big screen? Thanks Krish Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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tile and 2dlabels
by Krishnan Raman 29 Nov '22

29 Nov '22

Hi guys, Trying to show multiple binding protein sites on a large protein. Could successfully make footprints on the protein in different colors on the protein for different binding sites. Was trying to include binding constants as 2dlabels with each model protein. How to associate these labels with models to tile them along with the models? Combining the models (combine on (2dlabel model and structure models did not work.) Trying to use tile command with the 2dlabels to show IC50’s with the individual proteins. What is best way to do this… May be use the label command? Thanks Krish Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows CONFIDENTIALITY NOTICE This email, including any attachments, may contain confidential or legally privileged information that is intended only for the individual or entity to whom it is addressed. If you are not the intended recipient, please be advised that any dissemination, distribution or copying of this email and any attachment is strictly prohibited. If you have received this email in error, please reply to the sender so that BioCryst Pharmaceuticals, Inc. can take corrective measures and then permanently delete this email and any attachment, including any printed copies. Thank you.

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chimerax hbonds batch analysis
by Visvaldas K. 28 Nov '22

28 Nov '22

Dear ChimeraX wizards, I was trying to generate hbond analysis via nogui, by issuing "chimerax --nogui --script "myscript.cxc", where in the script I put the following commands: open /Users/visvaldas/temp0000.pdbselect /B hbonds sel saveFile /Users/visvaldas/temp00.hbonds restrict cross batch true quit However, something is wrong with hbonds line since I am getting this error:Executing: runscript myscript.cxc Traceback (most recent call last): File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/scripting.py", line 83, in open_python_script code = compile(data, stream.name, 'exec') File "myscript.cxc", line 4 hbonds sel saveFile /Users/visvaldas/temp00.hbonds restrict cross batch true ^ SyntaxError: invalid syntax What I am doing wrong? (Also, when using GUI, the hbonds line was much longer, so I deleted those reveal, color, etc entities to make it more relevant to batch. (The "long" line hbonds sel saveFile /Users/visvaldas/temp00.hbonds color #fffb00 dashes 5 restrict cross reveal true retainCurrent truefrom the GUI does not work either) Best wishes, Visvaldas

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Cα distance per residue in alignment
by Michael Habeck 28 Nov '22

28 Nov '22

Dear ChimeraX forum, I'm interested in getting the distance between Cα for all residues in an alignment. I've noticed that the Cα RMSD values in the txt file obtained from the header of the sequence alignment created by matchmaker via sequence header rmsd save are different from the distances measured using the rmsd or distance command. The Cα distance measured is approx. 41% higher across the entire alignment than in the saved output. When selecting a pair of aligned residues from the alignment viewer, the distance shown does not match the one in the output file but the distance measurement. I've attached a file with the respective distances for the alignment of chains A in 3c4f and 3gqi as an example. Not sure if this is a misunderstanding from my side or a bug, yet I'd greatly appreciate a clarification of the differences. With thanks in advance and best regards, Michael

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Align with specific atoms (but against all other molecules)
by Kim, Doo Nam 28 Nov '22

28 Nov '22

Hi, I’ve used align #2/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N align #3/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N align #4/X:1 @CA,O,C,N to #1/X:1 @CA,O,C,N … to align #2 molecule against #1 molecule with backbone atoms #3 molecule against #1 molecule with backbone atoms #4 molecule against #1 molecule with backbone atoms etc… However, how can I align all rest molecules (e.g. #2~#100) against #1 molecule with backbone atoms at once in chimeraX? I’ve used align all toAtoms #1 matchAtomNames true align all toAtoms #1 matchNumbering true to align all molecules to #1 molecule at once. However, with this command, I cannot specify to use backbone atoms (e.g. CA,O,C,N) only when aligning. I think that there should a 1 line command that aligns all molecules with specific atoms only or there is chimeraX equivalent python script as from chimera import runCommand as rc # use 'rc' as shorthand for runCommand from chimera import replyobj # for emitting status messages Best, Doo Nam

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input delay on one computer and only for ChimeraX
by Barbara S Holme 28 Nov '22

28 Nov '22

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Re: [chimerax-users] [Chimera-users] Writesel command in chimeraX
by Elaine Meng 27 Nov '22

27 Nov '22

Hi Prathvi, Please use the chimerax-users(a)cgl.ucsf.edu address to ask ChimeraX questions (instead of chimera-users(a)cgl.ucsf.edu) so that users will not be confused about which program we are discussing. In ChimeraX you can use the "info" command to report the selection to the Log, as detailed in this previous post. <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-July/003963.html> "info" help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html> It does not have an option to save a file. Instead you have to save the ChimeraX Log in another step. You can use "log clear" before you use "info" and then "log save" to save to HTML file. "log" help <https://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 26, 2022, at 5:04 AM, Prathvi Singh via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hi Elaine, > > Is the writesel command available in chimeraX because I could not find it in the Actions menu? > If not, then is any equivalent available apart from the command which saves selection as a new PDB file? > > Thanks once again in advance

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how to remove axes?
by Francisco Murphy Pérez 26 Nov '22

26 Nov '22

After loading a mtz file, 3 axes appear in the middle of the screen. How do I remove them? Thanks

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Display sequence alignment from structure alignment
by James H Naismith 25 Nov '22

25 Nov '22

In Chimera I can sort of print out a sequence alignment based on structural superposition. (Match-align) I can make a very nice structural superposition of very unrelated proteins with matchmaker, all I want to do is print out the resulting sequence alignment (where residues are with y A of each other) Any help gratefully received. With best wishes Jim Division of Structural Biology, Roosevelt Drive, Oxford, OX3 7BN james.naismith(a)strubi.ox.ac.uk Pronouns: he, him, his

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Opening .xyz file in ChimeraX
by Carina Luo 23 Nov '22

23 Nov '22

Hello, I am trying to open an .xyz file in ChimeraX. I installed SEQCROW (1.5.9) as prompted, but ChimeraX still says "Opener for format 'XYZ file' is not installed; see log for more info." Here is the output I got when I installed SEQCROW (1.5.9): Downloading bundle SEQCROW-1.5.9-py3-none-any.whl Errors may have occurred when running pip: pip standard error: --- [notice] A new release of pip available: 22.2.2 -> 22.3.1 [notice] To update, run: C:\Program Files\ChimeraX\bin\ChimeraX.exe -m pip install --upgrade pip --- pip standard output: --- Looking in indexes: https://pypi.org/simple, https://cxtoolshed.rbvi.ucsf.edu/pypi/ Processing c:\users\user\downloads\seqcrow-1.5.9-py3-none-any.whl Requirement already satisfied: jinja2 in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (3.1.2) Collecting Send2Trash Downloading Send2Trash-1.8.0-py3-none-any.whl (18 kB) Requirement already satisfied: ChimeraX-Core<=1.5,>=1.2 in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (1.5rc202210312311) Requirement already satisfied: scipy in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (1.9.0) Requirement already satisfied: psutil in c:\program files\chimerax\bin\lib\site-packages (from SEQCROW==1.5.9) (5.9.1) Requirement already satisfied: MarkupSafe>=2.0 in c:\program files\chimerax\bin\lib\site-packages (from jinja2->SEQCROW==1.5.9) (2.1.1) Requirement already satisfied: numpy<1.25.0,>=1.18.5 in c:\program files\chimerax\bin\lib\site-packages (from scipy->SEQCROW==1.5.9) (1.23.1) Installing collected packages: Send2Trash, SEQCROW Successfully installed SEQCROW-1.5.9 Send2Trash-1.8.0 Could you please help me figure out what I still need to do in order to successfully open .xyz files in ChimeraX? Sincerely, Carina

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How do you submit a sequence text file to BLAST/Modeller in ChimeraX?
by Ralph Loring 23 Nov '22

23 Nov '22

Hi, When I was using Chimera and wanted to use Modeller, I would go to sequence/Blast, paste in my sequence text file, Blast and then pick homologous structures and then connect to Modeller. Both Blast and Modeller appear to be present in ChimeraX, but I can't see how to enter my text file. Is everything supposed to go to AlphaFold now? Are there any tutorials on how to use Modeller in ChimeraX? Thanks! P.S. Hope you have a Happy Thanksgiving! I'm not planning on doing anything with this until after the holidays, so don't rush in answering. Ralph Lorini Ralph H. Loring Associate Professor of Pharmacology Department of Pharmaceutical Sciences 166 TF Northeastern University 360 Huntington Avenue Boston, MA 02115 USA 617-373-3216 office 617-373-8886 fax r.loring(a)northeastern.edu

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Developing a ChimeraX bundle - accessing programmatically ChimeraX(GUI open) session
by Stylianos Iliadis 23 Nov '22

23 Nov '22

Hello, I would like to develop a small bundle-plugin for automatically annotating residue labels in protein structures. I tried to access ChimeraX via command line when ChimeraX was running (GUI open) with an opened protein structure in order to study the structure objects hierarchy( chain ->residue ->atoms). This would help me understand it better and code accordingly. Unfortunately, I didn’t manage to do so. Could you please suggest me a way, a page or terminal where I could read more about the internal structure of ChimeraX and if possible to programmatically access a session when it’s running in ChimeraX. Kind regards, Stel Iliadis

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suggestion
by Hassan, Sergio (NIH/NIAID) [E] 22 Nov '22

22 Nov '22

Hello, I recently requested via Phil Cruz the 'tile' command, which I learned it was recently introduced. I have been using it successfully. However, there are two points I would like to bring to your attention (I asked Phil to ask you, but not sure he reached out) 1) when a session is saved as .cxs and I quit the program, after opening it again, the most important feature of the 'tile' command (rotations around each own axis) is lost. The tile distribution is still there, but now the entire thing rotates around a common axis. I need to apply 'tile' again to make it work, but this resets all the modifications I made in the saved session (these modifications include those in point 2 below). 2) any chance to add an argument to the 'tile' command so that the default spatial distribution, which assigns a 'distance' between near neighbors, can be adjusted with, say, 'zoom in" or "zoom out" or crowd in/out? I noticed the default puts each panel too far away from its neighbors for my taste, so I need to "move" them to make them look closer to one another. thanks s _____________________________________ Sergio A. Hassan https://bioinformatics.niaid.nih.gov/cmm/ BCBB/NIAID/NIH/DHHS 301 761 7221 (office) 301 741 5579 (mobile)

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Re: [chimerax-users] Export pLDDT scores
by Tom Goddard 22 Nov '22

22 Nov '22

Hi Asmahan, The pLDDT scores for an AlphaFold prediction are in the bfactor column of the PDB atomic model file. Here is an example of lines from such a file where the value 85.53 is the pLDDT for residue 1. ATOM 1 N ASP B 1 -0.818 -36.026 -12.912 1.00 85.53 N ATOM 2 CA ASP B 1 0.545 -35.783 -13.373 1.00 85.53 C ATOM 3 C ASP B 1 0.706 -34.352 -13.882 1.00 85.53 C The bfactor is assigned to every atom. But pLDDT is only assigned for each residue and measures CA position so you might want to look at only the CA lines. $ grep CA ~/Downloads/ChimeraX/AlphaFold/prediction_14/af252_unrelaxed_rank_1_model_2.pdb ATOM 2 CA ASP B 1 0.545 -35.783 -13.373 1.00 85.53 C ATOM 10 CA CYS B 2 1.983 -32.130 -13.721 1.00 95.45 C ATOM 16 CA PRO B 3 3.029 -30.770 -17.151 1.00 93.20 C ATOM 23 CA SER B 4 6.629 -31.094 -18.066 1.00 93.36 C You can also write the values into a ChimeraX attribute file using ChimeraX commands select #1@CA save ~/Desktop/plddt.defattr attrName bfactor models #1 selectedOnly true and that file looks like the following attribute: bfactor recipient: atoms match mode: 1-to-1 /A:1@CA 56.150001525878906 /A:2@CA 53.33000183105469 /A:3@CA 53.59000015258789 /A:4@CA 59.380001068115234 documentation here https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#attributes Tom > On Nov 22, 2022, at 7:08 AM, Asmahan Alghamdi <Asmahan.Alghamdi(a)nottingham.ac.uk> wrote: > > Dear Tom, > I hope you are well. I was wondering if there is away to export pLDDT scores of the best predicted model of a protein using ChimeraX e.g. 1.5 (which I am using in my investigations)? > > Thank you very much. > Asmahan

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Zoom over frames
by Krishnan Raman 21 Nov '22

21 Nov '22

Hi , Can I have the zoom command execute over several frames? Thanks Krish

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Re: [chimerax-users] [Chimera-users] Coloring the unit cell box
by Elaine Meng 21 Nov '22

21 Nov '22

(switching to chimerax-users address since this is all about ChimeraX, not Chimera) Sorry no, there is no linewidth setting on the unit cell outline box. However, you can "fake it" by selecting that model so that there are green outlines to show the selection, and then changing the selection-outline color and width: (1) select the outline box model, e.g. as described in the previous message by checking the selection box in the Model Panel (2) use "graphics selection" command to change the selection-outline color and thickness <https://rbvi.ucsf.edu/chimerax/docs/user/commands/graphics.html#selection> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Nov 18, 2022, at 9:12 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Thanks a lot, Elaine, this worked indeed! > Just one final point: how can I make the linewidth larger? When I make a picture, the thin lines of the box disappear. > I understand ChimeraX interpretes these lines as a surface, I can change the colour when choosing surface in the colour blow up. > > On 18/11/22 17:49, Elaine Meng wrote: >> Hi Xavier, >> As far as I can tell, it is exactly the same in ChimeraX as in Chimera. First, make sure you aren't using a very old version of ChimeraX. I tried it in ChimeraX 1.5 release candidate (2022-11-08) just now: >> >> - open your structure that has unit cell information, e.g. 1fav >> >> - in Unit Cell tool (menu: Tools... Higher-Order Structure... Unit Cell) click Outline to show unit cell box >> >> - if you want to change box outline color, can use the same method as described below for Chimera. I wasn't able to select it by Ctrl-click, however, so instead use the selection (hand with green dot) checkbox in the Model Panel to select it, then use Actions... Color... [...]. Or, you can just click the color square in the Model Panel and use the system color chooser to change the color interactively. Screenshot: >> >> <Screen Shot 2022-11-18 at 8.48.02 AM.png> >> >> >> I hope this helps, >> Elaine >> ----- >> Elaine C. Meng, Ph.D. >> UCSF Chimera(X) team >> Department of Pharmaceutical Chemistry >> University of California, San Francisco >> >> P.S. for ChimeraX questions specifically, you may want to use the other mailing list, chimerax-users(a)cgl.ucsf.edu >> >>> On Nov 18, 2022, at 7:03 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: >>> >>> Dear Elaine, >>> I am now trying to get this done in ChimeraX where there is indeed a similar option. Unfortunately, if I proceed as in the instructions >>> I do not get the cell box, in contrast with old Chimera. I also tried through the command line but unsuccessfully. >>> Am I missing something? >>> Thanks a lot in advance, >>> Xavier >>> >>> On 26/10/22 17:45, Elaine Meng wrote: >>>> Hi Xavier, >>>> You can select the box (Ctrl-click on it) and then use menu: Actions... Color... [choose color], then clear selection by Ctrl-click on blank area of window or menu Select... Clear Selection. >>>> I hope this helps, >>>> Elaine >>>> ----- >>>> Elaine C. Meng, Ph.D. >>>> UCSF Chimera(X) team >>>> Department of Pharmaceutical Chemistry >>>> University of California, San Francisco >>>> >>>> >>>>> On Oct 26, 2022, at 1:56 AM, F.Xavier Gomis-Rüth via Chimera-users <chimera-users(a)cgl.ucsf.edu> >>>>> wrote: >>>>> >>>>> Dear all, >>>>> is there a way in Chimera or ChimeraX to get the unit-cell box being drawn in another colour than white? >>>>> This forces the background to be dark.... >>>>> Thanks a lot in advance, >>>>> Xavier >>>>> >>> >> > > -- > <fxgr_signanew.jpg> > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users

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Re: [chimerax-users] [Chimera-users] Alphafold
by Tom Goddard 20 Nov '22

20 Nov '22

AlphaFold prediction is running fine in ChimeraX, just tested a monomer and heterodimer prediction in the ChimeraX release candidate. AlphaFold prediction is not available in the old Chimera software. You would have to give details such as the exact pasted error, the input you were running on, the ChimeraX version, and best to do that with ChimeraX menu Help / Report a Bug.... Tom > On Nov 19, 2022, at 11:38 PM, Kornelius Zeth via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Dear all – > > I’m using Alphafold in Chimera and I have a problem to run this properly on Colab. The people from Colab say that the error messages I get since recently are related to Alphafold developers having installed a new version. Could you please let me know what I could do to get the program running again? > > Thanks and have a nice day > > Kornelius > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> > Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users <https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users>

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Chimerax Error
by Natalie Loui 20 Nov '22

20 Nov '22

Hi all, I’m trying to visualize a capsid by using the sym command but I keep getting this error ”Assembly "1" not found, have" If you have any advice, please let me know. Natalie Loui PhD Student | Skaggs Graduate School of Chemical and Biological Sciences Email: nloui(a)scripps.edu | Phone #: (808)221-8270 Scripps Research Institute | 130 Scripps Way, Jupiter, FL 33458 | https://education.scripps.edu

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