November 2024 - ChimeraX-users - RBVI Mailing Lists

Generating quantitative values for electrostatic potential and molecular lipophilicity potential
by mishra.ananya.163＠gmail.com 06 Nov '24

06 Nov '24

Dear Sir/Madam, I hope this message finds you well. My name is Ananya, and I am an undergraduate student working on a project analysing protein structures. I am currently exploring the tools available in ChimeraX to measure structural parameters of protein models. I find the visualization features for surface electrostatic potential and molecular lipophilicity potential especially valuable for my research, as they provide essential insights for my analyses. However, I have encountered some difficulty in locating a way to export quantitative values for these surface properties. Could you please advise if there is a method within ChimeraX to generate and export these values? Thank you for your time and I would greatly appreciate any guidance you could offer. Hope you have a great day ahead! Best regards, Ananya

3 8

integration of US-align into ChimeraX
by Chengxin Zhang 06 Nov '24

06 Nov '24

Dear ChimeraX developer. I am the developer of the US-align tool for protein and nucleic acid structure alignment. We currently offer a command line tool and a plugin for PyMOL. We are asked by the community to make a ChimeraX plugin. I have used ChimeraX for cryo-EM structure analysis before and know that there is a related tool called matchmaker. However, I do not know where to start to implement a matchmaker-like plugin for US-align in ChimeraX. Can you give me some recommendations and/or point me to a developer I can work with? Thanks. Chengxin Zhang, PhD Research Assistant Professor Department of Computational Medicine & Bioinformatics University of Michigan, Ann Arbor, MI

2 1

Variables and conditional statements in the command line
by Roden Deng Luo 06 Nov '24

06 Nov '24

Hello again, Are variables and conditional statements possible in the command line in any way? Thanks, 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.

2 2

Troubleshooting the match function
by Christman, Nick 04 Nov '24

04 Nov '24

Hello, My name is Nick Christman and I am a microbiology PhD student at Indiana University. I am using ChimeraX to visualize and compare some small proteins (minor pilins) and it has been working great. I have run into an issue that I am hoping you can help me resolve. I want to use the match function to compare various different minor pilins. Each minor pilin has a somewhat unique structure, and I am trying to make the case that certain minor pilins from one organism are homologous to other minor pilins from a different organism. I have noticed that the match function provides different results from session to session. This concerns me and makes me question how much I can trust the results provided by chimeraX. Along with different spatial matching, the calculated RMSD values differ greatly. Is there a way I can make these matches more consistent? Like dictating a set starting point for matching? Thanks for your time! Nick Christman (He/Him) Dalia Lab Indiana University

2 1

setzoom command in Chimera X
by Vitali James 04 Nov '24

04 Nov '24

Dear Chimera support, There was a some old code to set the zoom in the chimera. I would like to set the same frame size of different models and different views in chimerax. How it can be done in chimeraX. best, James

2 1

Tool docking
by Eric Pettersen 02 Nov '24

02 Nov '24

Hi all, Starting with tomorrow’s daily build (but not the 1.9 release candidate or [eventual] production release), most tools can no longer be docked into the top or bottom areas of the main window, just the sides. This should prevent a lot of accidental grief from accidentally docking a tool into the toolbar area. This policy can be overridden by the tools themselves if typical use of that tool might involve docking into the top or bottom areas. Initially, two tools override the policy: the sequence viewer can be docked anywhere (since you might want it as wide as possible), and the tool created by the buttonpanel command can be docked into the top area, so that it can be placed next to the toolbar. If there are other tools that can really benefit from being docked into the top or bottom areas, please let me know. --Eric Eric Pettersen UCSF Computer Graphics Lab

2 2

Using name of selection with rmsd command
by Alexander Lee 01 Nov '24

01 Nov '24

Hello! I've been trying to use "sel sel res t; ~sel H; ~sel @N,CA,C,O; name target sel; sel #2:23; ~sel H; ~sel @N,CA,C,O; name original sel; rmsd target to original" to find the RMSD of just the target's side chain to the original, but I keep getting a reported RMSD of 0.000. I click on an atom of the target residue, then use "sel sel res t" to select the whole residue, "~sel H" to deselect hydrogens, " and "~sel @N,CA,C,O" to deselect the backbone. I then name the left-over selections. I thought this series of commands would work but it's giving me an incorrect RMSD. Is there a different combination I should try? Thank you, Alex

2 2