- ChimeraX-users - RBVI Mailing Lists

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

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Variables and conditional statements in the command line
by Roden Deng Luo 05 Nov '24

05 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.

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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

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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

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Tool docking
by Eric Pettersen 01 Nov '24

01 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

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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

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Coloring surface patches
by Radoslav Krivak 31 Oct '24

31 Oct '24

Hi I'm struggling with the following task. I want to display protein surface and color specific surface patches. More precisely, I want to: For each surface patch: 1. select specific solvent exposed atoms (by "Atom serial number" column from pdb file) 2. assign their surface a custom color (different color for each patch) A surface patch can contain atoms from 2 or more chains. Basically I'm trying to achieve something that looks like this: https://raw.githubusercontent.com/rdk/p2rank/refs/heads/develop/misc/img/p2… Is that even possible in ChimeraX? If it's not possible to select specific atoms by atom serial number I'd like to do it at least for residues. I’d be grateful for any help. Best regards Radoslav Krivak

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Re: Smooth-MD script for a trajectory visualisation
by Enrico Martinez 29 Oct '24

29 Oct '24

Hello Eric, Just one extra question about the Smooth-MD script :-) Would it be possible to extend the idea of different smooth windows on different selections within the same model id (besides the version that we discussed applying for several different models).. For example, I have a complex system composed of membrane protein bound to a ligand embedded in explicit water and lipids. So, I divided all the components according to three different selections, which I would like smooth differently, in the following way: 1) protein & ligand (protein | :LIG) --> smooth with 5 windows 2) lipids according to amber naming (:PC,PE,PS, OL,PA) smooth with 6 windows 3) water and ions (:WAT|:NA*|:Cl*) smooth with 7 windows Would it be possible to do such tricky things using the same script? Many thanks in advance ! Enrico Il giorno sab 19 ott 2024 alle ore 02:55 Eric Pettersen <pett(a)cgl.ucsf.edu> ha scritto: > Hi Enrico, > Our servers have been down this week, so this is my first opportunity to > respond. So one possible approach is to change the "window = 10" line to: > > window_by_id = { (1,): 5, (2,): 10 } > > and change the 'if/continue' statement just inside the loop to: > > try: > window = window_by_id[s.id] > except KeyError: > continue > > The 'id' attribute of a model is a tuple of the model ID numbers, so for > model #1 it would be (1,), for model #2.2.1 it would be (2,2,1), etc. > So the try/except clause skips all models other than the ones you > explicitly put in the window_by_id dictionary. > > --Eric > > On Oct 11, 2024, at 1:32 PM, Enrico Martinez <jmsstarlight(a)gmail.com> > wrote: > > Hello Eric, > > I have an extra question about the Smooth MD script: I modified it abit to > apply the smoth effect only on a model with the name "ottimo.pdb" so that > it will affect only one selected model ( in the case when there are several > models in the same session ..) Here is this version enclosed. > > Could you suggest how it could be further modified to affect e.g. 2 models > via 2 different smooth windows e.g. smooth the model with the id 1 window=5 > and smooth the model with the id 2 with window2=10 ? > > Many thanks for help! > > Enrico > > Il giorno ven 8 dic 2023 alle ore 16:10 Enrico Martinez < > jmsstarlight(a)gmail.com> ha scritto: > >> Thank you very much Eric ! >> >> Cheers >> >> Enrico >> >> Le mer. 6 déc. 2023 à 19:02, Eric Pettersen <pett(a)cgl.ucsf.edu> a écrit : >> >>> Hi Enrico, >>> I have updated the smoothing script on the Scripts >>> <https://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts> page. If you get >>> a new version, there is a line near the top ("stride = 1") that you can >>> edit to make it use, say, every 5th frame ("stride = 5"). One issue is >>> that the coordinate set slider doesn't properly react to the change in the >>> number of frames. You have to close the slider and open a new one >>> ("coordset slider #1"). I will look into fixing that. >>> >>> --Eric >>> >>> On Dec 6, 2023, at 1:34 AM, Enrico Martinez via ChimeraX-users < >>> chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> and generally it would be visually fine with averaging of every N frame ? >>> well it would be interesting to test anyway :-) >>> >>> Cheers >>> >>> Enrico >>> >>> Il giorno mar 5 dic 2023 alle ore 19:30 Eric Pettersen >>> <pett(a)cgl.ucsf.edu> ha scritto: >>> >>> >>> Well, the smoothing script temporarily takes about triple the memory use >>> of the baseline trajectory, so I can imagine it crashing for a large >>> trajectory. Do you need 1000 frames? I could change the script to use >>> every Nth frame, which would use a lot less memory... >>> >>> --Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>> >>> On Dec 5, 2023, at 7:13 AM, Enrico Martinez via ChimeraX-users < >>> chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> update: I've just got a crash with md-smooth py script on chimera-x >>> working on a big system with > 1000 frames loaded in a single pdb >>> (with smaller trajectory there is no issues ..) >>> >>> Enrico >>> >>> Il giorno mer 15 nov 2023 alle ore 18:53 Eric Pettersen >>> <pett(a)cgl.ucsf.edu> ha scritto: >>> >>> >>> You are welcome. >>> >>> I don't think there is a "right" value for the window. A larger value >>> will provide more smoothing, while also creating more non-physical >>> geometries for highly mobile parts of the structure. A judgement call >>> really. >>> >>> --Eric >>> >>> On Nov 15, 2023, at 3:33 AM, Enrico Martinez via ChimeraX-users < >>> chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> Gotcha, thank you very much Eric ! >>> >>> BTW what is the value for the window that should be used ? Does it >>> mean that the higher value would result in smoother dynamics ? >>> >>> Enrico >>> >>> Il giorno mar 14 nov 2023 alle ore 19:47 Eric Pettersen >>> <pett(a)cgl.ucsf.edu> ha scritto: >>> >>> >>> Hi Enrico, >>> I don't see how you could get that error. I couldn't reproduce it >>> myself. I would need some kind of recipe for how you get it to occur. A >>> separate problem is that the averaging in the script isn't really right. >>> Line 21 of the script should be changed from: >>> >>> weight = window + 1 + abs(i-j) >>> >>> to: >>> >>> weight = window + 1 - abs(i-j) >>> >>> i.e. change the "+ abs(...)" to "- abs(...)". I have corrected the >>> script on the Scripts page. >>> >>> --Eric >>> >>> Eric Pettersen >>> UCSF Computer Graphics Lab >>> >>> >>> On Nov 14, 2023, at 6:31 AM, Enrico Martinez via ChimeraX-users < >>> chimerax-users(a)cgl.ucsf.edu> wrote: >>> >>> update: i've just opened closed chimera-x and reloaded my pdb and >>> everything works as expected. probably there is a bug somewhere .. >>> >>> Il giorno mar 14 nov 2023 alle ore 14:56 Enrico Martinez >>> <jmsstarlight(a)gmail.com> ha scritto: >>> >>> >>> Dear Chimera-X users. >>> >>> I am trying to record a md trajectory loaded as multi-pdb file: >>> >>> open ./stripped_traj2.pdb coordsets true >>> >>> I have the issue with smooth-md script (enclosed), which produces the >>> following error: >>> >>> open smooth_md_chX.py >>> open /home/test/Bureau/MOVIE_CHIMERAX\/smooth_md_chX.pyTraceback (most >>> recent call last): >>> File "/home/test/Bureau/MOVIE_CHIMERAX\/smooth_md_chX.py", line 23, in >>> <module> >>> avg += weight * coord_sets[j] >>> ValueError: operands could not be broadcast together with shapes >>> (6120,3) (6112,3) (6120,3) >>> >>> Should something be fixed in the script in order that I could observe >>> the MD movie with smooth details ? >>> >>> Thank you in advance >>> >>> Enrico >>> >>> _______________________________________________ >>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>> Archives: >>> https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>> >>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>> Archives: >>> https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>> >>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>> Archives: >>> https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>> >>> >>> >>> _______________________________________________ >>> ChimeraX-users mailing list -- chimerax-users(a)cgl.ucsf.edu >>> To unsubscribe send an email to chimerax-users-leave(a)cgl.ucsf.edu >>> Archives: >>> https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ >>> >>> >>> >

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Sequence alignment and Extraction
by Mamadou Sangare 25 Oct '24

25 Oct '24

Dear, I would like to align two protein structures A and B, select and extract the parts of the B sequence that match A in a fasta file. Thank you for your support.

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Visualisation of water near protein
by Enrico Martinez 25 Oct '24

25 Oct '24

Dear Chimera X users ! I have a question about the visualization of water around the protein. When I open the pdb + trajectory of the whale system, ChimeraX masks most of the water box, only showing some selected water molecules (probably involved in the interactions with the protein). Then, viewing the MD system, I can observe an exchange of this water, which is great ! Would it be possible via some command to modify the number of the displayed water in the beginning of simulation e.g. showing more water observed in the proximity to protein (..but still not the whole water box !) ? Many thanks in advance Enrico

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