- ChimeraX-users - RBVI Mailing Lists

Question on Contacts and Distances Tools
by Haleh Shahbazi 05 May '23

05 May '23

Hello, I am using ChimeraX under “version 1.6rc202304182023 (2023-04-18)” and contacting you regarding contacts and distances tools I am working on analyzing biological assembly PDB files including two chains. Simply, I want to identify / calculate distance between residues within each chain and across two chains separately – In the other word, display interchain and intrachain residue distance. To get that done, I’ve already explored “Distances” and “Contacts” tools under “Structure Analysis” but I have difficulty with identifying interchain residue distances and also understanding all those features / options provided. Thanks in advance for your support! Haleh HALEH SHAHBAZI PHD STUDENT @GARTON LAB • she/her • [Personal/Lab LinkedIn] <https://www.linkedin.com/in/haleh-shahbazi> IBME, University of Toronto haleh.shahbazi(a)mail.utoronto.ca<mailto:haleh.shahbazi@mail.utoronto.ca> www.gartonlab.org<http://www.gartonlab.org/> • bme.utoronto.ca<https://bme.utoronto.ca> • [LinkedIn] <https://www.linkedin.com/school/bme-uoft> [Twitter] <https://twitter.com/bme_uoft> [Instagram] <https://www.instagram.com/bme_uoft/> [signature_283494549]<https://bme.utoronto.ca/>

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Web site downtime
by Eric Pettersen 04 May '23

04 May '23

Hi all, Due to a scheduled power outage at UCSF followed by server upgrades, the ChimeraX website and web services will be unavailable from Tuesday May 16 through most of Wednesday May 17. Please pardon any inconvenience, --Eric Eric Pettersen UCSF Computer Graphics Lab

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Re: [chimerax-users] Merging and covalently joining two pdb's together in chimeraX
by Elaine Meng 04 May '23

04 May '23

Hi Rayees, For the best chance at getting a good answer, we recommend sending ChimeraX questions to the chimerax-users list (CC'd here) unless you are including private data. If the two models are already positioned appropriately to form the bond, you could first combine them into a single model and then add a bond (e.g. "bond" command or Build Structure tool, Adjust Bonds section). <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/bond.html> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#bonds> However, if you didn't necessarily put the models in the right place to form the bond, you can use "build join" which will include all of the following: moving one model to the appropriate position to form the bond, combining the models into one, and forming the bond. You cannot use "build join" if the models are already combined or if you don't want the models to move relative to each other. There is also a graphical interface to "build join," which is the Build Structure tool, Join Models section. <https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/build.html#join> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html#join> You can open the Build Structure from the menu under Tools... Structure Editing. <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/buildstructure.html> I don't know much about refinement, but sounds like you should take a look at the ISOLDE plugin for ChimeraX. <https://cxtoolshed.rbvi.ucsf.edu/apps/chimeraxisolde> <https://isolde.cimr.cam.ac.uk/> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On May 4, 2023, at 11:24 AM, Rayees Mattoo <rmattoo(a)stanford.edu> wrote: > > Hi Elaine, > I am trying to merge two models (say #1 and #2) and join the two models with a covalent bond at amino acid residue number say 240 (#1)and 241 (#2). I first combined the two models (#1 and #2) using combine command. However, when I use build join command it does not seem to work. Is there a better way to covalently join two models in chimeraX? > > Also, is there a way to refine models in chimeraX like Real Space refine in Coot? > > Thanks > > Rayees

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Info on ChimeraX
by Fabrizio Fierro 04 May '23

04 May '23

Hi, I work for a startup called Protai and I am interested in ChimeraX. 1) Are all the functions available in Chimera implemented also in ChimeraX? 2) Specifically, with Chimera it was easy to load, visualize and work with cryoEM maps. Does ChimeraX work in the same way? 3) Would it be possible to get a free trial period for ChimeraX? Thanks, Fabrizio Fierro.

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Installing other python packages in chimeraX
by Shubham Devesh Ramgoolam 03 May '23

03 May '23

Dear ChimeraX team, I have some python scripts for performing computation using chimeraX in the nogui mode. Those scripts rely on packages not available in the python environment of chimeraX and I installed them using: ChimeraX-console.exe -m pip install add_package --user I intend to distribute my scripts to other users and they will also need to install these packages. As such, I have written another python script to automate the installation of these packages (the path to ChimeraX-console.exe (if Windows) or ChimeraX.exe (if Mac) must be supplied in a text file for this to work). The heart of the automation script is as follows: for item in list_packages: subprocess.call([path_chimeraX, '-m', 'pip', 'install', item, '--user']) Is this approach of installing python modules in chimeraX valid, considering that different users may have a different environment for their chimeraX? (I am worried that pip install might not work on some setups.) Regards, Shubham Ramgoolam Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

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Question about viewing chain pdb in ChimeraX
by Thu Nguyen 02 May '23

02 May '23

Hello, I am using ChimeraX to save the .pdb file of chains in a protein. Here are my commands: +) open 7oci +) select #1/E + save /.../E.pdb model #1 selectedOnly true Then I opened that E.pdb model in ChimeraX and saw that chain E only contains helices. However, when I checked the .pdb file of chain E in a text editor, I saw that it contains sheets as well. The number of sheets are even larger (Number of helices: 52, sheets: 76). Do you know the reason why I don't see the sheets of chain E in ChimeraX? Am I missing something? I have attached the screenshots and the pdb of chain E. I took this chain from the pdb ID 7oci. Thank you very much. I am looking forward to hearing from you. Best regards, Thu

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Virtual Crash Course - Understanding PDBx/mmCIF | Tomorrow, May 3rd | REGISTER NOW!
by Brian Hudson 02 May '23

02 May '23

Virtual Crash Course The RCSB Protein Data Bank will provide a course, "Use PDB data to their full extent: Understanding PDBx/mmCIF" on Wednesday, May 3rd 2023 from 1:00-3:00 EDT Understand the basics of PDBx/mmCIF data dictionary and file format that underpin archiving of more than 200,000 experimentally determined three-dimensional biostructures in the PDB. Learn about software tools for generating and working with PDBx/mmCIF files, and programmatic access for harvesting PDB data. The program: https://iqb.rutgers.edu/sites/iqb.rutgers.edu/files/crashcourses/mmCIF-cras… Free registration: https://go.rutgers.edu/u3vpwjet If you have questions, please contact Michelle Sanghera: msanghera(a)iqb.rutgers.edu

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Plugin development: how to install python packages
by BARRY E DEZONIA 01 May '23

01 May '23

Hello, I am developing a chimerax plugin. My code will have some interaction with mdtraj. I need mdtraj to be installed in the python that ships with chimerax. I tried "chimerax -m pip install mdtraj" but I get all kinds of error dialogs popping up in the chimerax instance that gets launched during the installation. I terminate all the error dialogs and then exit chimerax (as the python install seems frozen) and then it indeed says installation has failed and gives unusual error messages (like setuptools was less than version 48.0.0 while chimerax reports it to be 65.x.y and even 66.x.y after upgrading). Can someone tell me the correct syntax to use to install mdtraj in chimerax's python? Thank you.

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How to update the bonding status every frame when viewing a molecular dynamic trajectory?
by 洪冉 30 Apr '23

30 Apr '23

Dear users and developers of ChimeraX, Recently I want to produce some decent movies of a molecular dynamic trajectory, I loaded the pdb file and the trr file into ChimeraX. Everything goes well until some bond broken occurred, the display became very strange since the bond was stretched to an unreasonable length. I have been told a solution by using ~bond, bond #1 to fix the issues. However, it is impossible to do it at every frame when you have to record a movie and your trajectory was with thousands of frames. Thus, I ask for help, is there a solution to update the bonding status of every frame automatically? Yours, Ran

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How to install the "SEQCROW bundle" plug-in for xyz file in ChimeraX1.5?
by 洪冉 28 Apr '23

28 Apr '23

Dear ChimeraX Developers and Users, I want to view some quantum chemical results from ORCA calculation, and information popped up from ChimeraX telling me that I must install a plug-in called "SEQCROW bundle" for this purpose. However, due to some well-known reasons, I can not fetch this plug-in with the built-in method 'Tools-More Tools'. I think I have to do it in a manual way. Could anyone send me a related file to install this plug-in with a guide showing me how to do it in a manual way. Thanks in advance. Yours, Ran Apri 28 2023

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Python scripts while running MD
by Rafael Rocha 26 Apr '23

26 Apr '23

Dear chimera users! During a molecular dynamics simulation, I would like to run a python script that triggers a specific command once the simulation has reached a certain number of steps or a specific amount of time. I was able to programmatically start, pause, continue and stop a simulation using a primary Isolde object. However, it appears that the script is not waiting until the maximum number of MD steps is reached before moving on to the next command. I've tried using the sleep() python command, but unfortunately, this causes chimeraX to get stuck and unresponsive until the script is finished sleeping. Do you have any suggestions for how I can achieve this without causing chimeraX to freeze up? Thank you for your help! -- Rafael E. O. Rocha, Ph. D. Department of Biological Sciences Federal University of Minas Gerais.

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Manual Averaging Enquiry
by Lenka Milojevic 24 Apr '23

24 Apr '23

Hello! I'd appreciate it if you could detail how manual averaging of multiple .mrc maps can be done in ChimeraX. Thank you for your time. Sincerely, Lenka

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Enquires about predicting protein interaction with chimeraX/AlphaFold
by Yiling Lan 21 Apr '23

21 Apr '23

Dear ChimeraX Developers, Hope this email finds you well. I'm currently trying to predict the interaction of 2 proteins after watching the videos on youtube (Running AlphaFold to Predict Protein Complexes from ChimeraX). after installing the CimeraX (UCSF ChimeraX version: 1.6rc202304140213 (2023-04-14) version) but I did not see the check box for "Is prokaryotes? used for predicting complex). May I ask if in newer version the check box for complex prediction is at somewhere else? If it does not bother too much, could you please let me know if there is anyway I can run complex prediction on 1.6rc? Thank you so much. Best Wishes Yiling Lan

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Tunnel visualisation
by Kelly May Frain 20 Apr '23

20 Apr '23

Hello, I am using ChimeraX to visualise a tunnel found in my membrane protein using caver. I can put together the protein pdb and tunnel pdb perfectly. However, crucial to the figure is how the tunnel has a different radius throughout. In PyMol I can see this, but when I set the tunnel to sphere in chimeraX, it’s continuously the same diameter. I can change the colouring to b-factor and here it acknowledges the atom b factor range of 0.8 - 4-8 but I want to visualise the differences. Please can someone help me with a command? BW, Kelly

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Hopefully simple plugin development question
by BARRY E DEZONIA 19 Apr '23

19 Apr '23

Hello, I am looking at writing a plugin for chimerax that takes a pdb and runs some python code that will calc some stuff hand stuff to other programs. I know how to do this. What I want to know is how to find the current model's name / associated pdb filename from my plugin. Imagine my plugin really is just a "Run" button that looks up the current model, generates the associated pdb filename, and passes that name to my python script. Can someone tell me how in a chimerax plugin I can make the call that will give me the pdb filename I want? I've read much of the developer docs and could not find what I was looking for.

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Unable to select individual glycans in ChimeraX
by Coillie, Julie van 19 Apr '23

19 Apr '23

Dear ChimeraX, Is there any way to select one individual glycan on a crystal structure? The crystal structures I'm working with have multiple domains, each with glycans. I want to annotate the glycan per domain (every domain & glycan in a specific color). However, I can't edit individual glycan structures. The glycans are grouped under Non-standard residues, e.g. MAN, NAG, ... However, when selecting e.g. MAN, all the MAN structures light up, which are found on all 3 domains. An alternative would be using the sequence and annotating each individual sugar by using "select". However, these Non-standard residues are not in the sequence (they are when uploading this in Pymol), so I don't know a position to select them on. Is there a way to find the "sequence" for non-standard residues or any other way to annotate an individual glycan. Thank you in advance, Julie Van Coillie ________________________________ Disclaimer: http://www.sanquin.nl/e-maildisclaimer ________________________________

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Command use
by Wojciech Witek 19 Apr '23

19 Apr '23

Dear ChimeraX Team, I am trying to change this mesh properites because it covers the ligand too much (attachment). I wanted to make the lines thinner or transparent or divided in different ways. I could not find anything in the GUI so I searched for commands but apparently I use them wrong. Could you please guide me on how to use commands, let's say like this one : surfaceSmoothing true | false? If I type "true", I see an error in the log file. Where can I find what arguments should be use with a specific function?I had the same struggle with depth cueing, ribbon style edition and many other functions. ChimeraX is a great software but using GUI is so much easier to get familiar with, learn and utilize changes, comparing to command line. See attached file containing ligand, mesh and a log full of errors from pasted commands. Please, keep it confident because it is unpublished yet. Regards, Wojciech Witek -- Logo *Wojciech Witek* *| PhD Student Department of Structural Biology of Eukaryotes* Institute of Bioorganic Chemistry, Polish Academy of Sciences Noskowskiego 12/14 | 61-704, Poznań *email:*wwitek@ibch.poznan.pl *tel.:*61 852 85 03 *int.:*1347 **** ** facebook <https://www.facebook.com/ICHBPAN> twitter <https://twitter.com/ICHBPAN> instagram <instagram.com/ichbpan> WWW <https://portal.ichb.pl/>

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deleting alternate locations
by Elaine Meng 18 Apr '23

18 Apr '23

> On Apr 18, 2023, at 3:07 AM, Yu GUO 郭宇 <guoyu60(a)westlake.edu.cn> wrote: > > Dear, > > I am using Chimera/ChimeraX. I have 2 questions: > > I cannot open ChimeraX (win10 version) recently. Is there any problem in the server? > > I have a PDB file with two structural populations. In Chimera, how to delete the part with fewer population (say 40%)? I rememer it can be realized in the command line, but I forgot. > > Best wishes > Dear Sir, In the future, please use the following addresses (CC'd here) for general questions about the programs: chimerax-users(a)cgl.ucsf.edu for ChimeraX questions chimera-users(a)cgl.ucsf.edu for Chimera questions (where you sent this question is for commercial licensing questions -- thanks) (1) after you download the program, it does not depend on our servers to start. The issue is something with your own setup. The most likely problem is that you need to update your graphics driver but we would need more information from you to say anything else. (2) if you mean atomic occupancy, - in Chimera you can use Dock Prep (menu: Tools... Structure Editing... Dock Prep) and turn on the option "If alternate locations, keep only highest occupancy". You can turn off all the other options if you want. <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/dockprep/dockpre…> - in ChimeraX, it is not currently in the Dock Prep GUI, but you can use the "altlocs clean" command which would delete all the altlocs that are not currently used. By default, the highest-occupancy ones are the ones that are used, so this would delete the lower-occupancy ones (e.g. your 40%). You can change which altlocs are used with "altlocs change" and show a list of them with "altlocs list" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/altlocs.html#clean> If you need a PDB file then you can save PDB in a separate step, e.g. using File menu or a command. 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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Permission denied to "Spin Movie"
by Pam Cook 17 Apr '23

17 Apr '23

Hi, I just installed ChimeraX on macOS Catalina 10.15.7. During installation, it asked me to allow access to desktop files and I said NO. But now, when I try to create a SpinMovie file, I get the message: Permission denied reading directory "/Users/pam/Desktop" while trying to determine next unused file name movie#.mp4. I guess I should have said YES to the question above. How can I fix this? Thanks, Pam

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Question about using ChimeraX
by 韩磊 17 Apr '23

17 Apr '23

Dear Sir， I hope this mail finds you well. I am a professional researcher from Tianjin Medical University, China. I have encountered some difficulties in learning to use ChimeraX software. First, I would like to know if the software can be used to construct a graph of the process of channeling proteins from closed to open state (e.g., Appendix ). Second, we can currently only download and import a model of the closed state of a protein into the software, but it does not reflect its conformational changes, so I would like to know which option within the software can change the conformation of the protein. Sincerely yours, Lei Han, Ph.D. Tianjin Neurological Institute, Tianjin Medical University General Hospital, 154 Anshan Road, Heping District, Tianjin 300052, China

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Could you please inform the best advice to solve a structure via colabfold when GPU is an issue? I tried some routes already.
by Josh Gutierrez 14 Apr '23

14 Apr '23

Hello, I recently submitted a job through ChimeriaX and used the "prediction" task for it to be solved via Alphafold2-- the sequence is about 1300 amino acids in length. However, the protein could not be solved by alphafold2 and the colabfold reports the GPU consumption is too high for the structure to be solved. To resolve the problem, I tried breaking the sequence into two to solve this expected bimodal protein individually (into two separate structural parts) and even in combination purchased "compute units" for more memory and storage to do this, but the structure can't be solved without high predicted error. Please let me know what you think may resolve this issue. Currently, I am working with an external professor who may be able to connect me with a collaborator on this issue at UCSF if there is a cluster or core we can use to expedite the process to solve this structure I am addressing. Please let me know your thoughts at your earliest convenience. Please also let me know if you need any more information! Many thanks, Josh Gutierrez

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Measure inertia and measure center on aligned density maps and models
by Kevin Felt 13 Apr '23

13 Apr '23

Dear developers, I am trying to compare the center of mass of multiple cryo-EM maps and models. The receptor is the same in all cases, just the ligand bound in the binding pocket varies. I want to show a directionality to how the ligands are binding in the pocket between the structures, so I have aligned the maps and models together and am attempting to run "measure center" and "measure inertia" to initiate this comparison. However, when I run these commands, the output markers and ellipsoids are not positioned in an aligned fashion as their parent objects, but rather in there initial positions before alignment, which is not useful for comparisons of the subtle movements between structures. Additionally, if I could get the measurements to work on the aligned structures, is there a tool in ChimeraX that would allow me to draw vectors from a reference point to the center of masses? Furthermore, is center of mass the correct parameter for comparison of densities that are variable in shape? (e.g. comparing the relative position of a long and flat density to a short a globular density?) Thank you! Sincerely, -- Kevin C. Felt PhD Candidate - Chakrapani Lab Department of Physiology and Biophysics School of Medicine Case Western Reserve University

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Modeling post-translational modifications
by Guillaume Gaullier 13 Apr '23

13 Apr '23

Hello chimerax-users, I am trying to model a PTM, and the most sensible way to me seems to use the swapaa command and specify the sensible monomer from the PDB Chemical Component Dictionary as the target residue. Here is what I tried (residue #1/a:9 is a Lys): open 1kx5 swapaa #1/a:9 KCX And the error I got: Dynameomics rotamer library does not support KCX I tried all the rotamer libraries listed in the swapaa help page ( https://www.cgl.ucsf.edu/chimerax/docs/user/commands/swapaa.html#rotLib ), but none of them can provide stereochemical info for KCX. I can open the monomer I want (carbamylated Lys) with: open ccd:KCX But of course in this case it’s floating by itself as a new model, not incorporated in the protein sequence and structure I am interested in. Is this the correct way to model a PTM? If it is, where can I find a rotamer library that will contain the stereochemical info for KCX, and how do I tell ChimeraX to use it? If it is not how modelling a PTM is done, then how else should I do this? Thank you in advance, Guillaume När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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unifold
by Roger Leng 12 Apr '23

12 Apr '23

Dear Administrators, Is it possible to add "unifold" in your prediction, just like Alphafold? Thank you. Sincerely, Roger Leng

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Problem Installing ChimeraX
by Stephen P. Molnar 12 Apr '23

12 Apr '23

I am running an up-to-date installation of Debian Bullseye on my Linux platform. My attempt to install ucsf-chimerax_1.5ubuntu20.04_amd64.deb generated an interesting error message: sudo apt install ucsf-chimerax_1.5ubuntu20.04_amd64.deb [sudo] password for comp: Reading package lists... Done Building dependency tree... Done Reading state information... Done E: Unable to locate package ucsf-chimerax_1.5ubuntu20.04_amd64.deb I have managed to install Chimera, both Linux and Windows versions, many times without any problems. Guidance would be much appreciated. Thanks in advance, -- Stephen P. Molnar, Ph.D. https://insilicochemistry.net (614)312-7528 (c) Skype: smolnar1

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