- ChimeraX-users - RBVI Mailing Lists

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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