- ChimeraX-users - RBVI Mailing Lists

ChimeraX question
by Meden Isaac-Lam 30 May '24

30 May '24

Hello UCSF Chimera Team, I used Chimera and AutoDock Vina about 2 years ago. I just downloaded ChimeraX and I am trying to learn it. However, I forgot how to link AutoDock Vina. In the previous Chimera, it was under Tools and Surface Binding Analysis. Any suggestion on how to do it? Thanks. Your assistance is greatly appreciated. Sincerely, Meden F. Isaac-Lam Purdue University Northwest

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Error installing bundle: No module named pandas
by Ricardo Righetto 29 May '24

29 May '24

Hi, Not sure if this should be reported here or to the bundle developers directly, but in any case here it goes: When trying to install the ArtiaX plugin on ChimeraX v1.7.1 on Ubuntu 22.04 from the toolshed (both via command line and through the GUI) I ran into the following error: *** error: subprocess-exited-with-error × python setup.py egg*info did not run successfully. │ exit code: 1 ╰─> [10 lines of output] Traceback (most recent call last): File "", line 2, in File "", line 34, in File "/tmp/pip-install-ni7khioh/starfileddcd2480b29b4cad9233c413b6568ba0/setup.py", line 2, in from starfile.version import VERSION File "/tmp/pip-install-ni7khioh/starfile_ddcd2480b29b4cad9233c413b6568ba0/starfile/__init* .py", line 1, in from .functions import open, read, new, write, version, star2excel File "/tmp/pip-install-ni7khioh/starfile _ddcd2480b29b4cad9233c413b6568ba0/starfile/functions.py", line 3, in import pandas as pd ModuleNotFoundError: No module named 'pandas' [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: metadata-generation-failed × Encountered error while generating package metadata. ╰─> See above for output. note: This is an issue with the package mentioned above, not pip. hint: See above for details . *** That is, it was complaining that the pandas package was missing when trying to install the starfile package, which in turn is a dependency of ArtiaX. I'm puzzled why it wasn't able to install pandas by itself, since it is listed as a dependency of starfile. Anyway, after trying many different things, I found out that I could install pandas via pip directly through the ChimeraX command line interface: pip install pandas And after that the bundle installation worked just fine. Not sure what to make of this, but maybe it's useful to developers or other users running into the same issue. Thank you, -- Ricardo Diogo Righetto

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Question Regarding rangecolor kdHydrophobic command
by Knotts, Garrett 29 May '24

29 May '24

Good morning, I am in the process of switching over from Chimera to ChimeraX. I have found ChimeraX to be incredibly more user friendly and well-designed. I wanted to reach out regarding the rangecolor kdHydrophobic command. I often use this command in chimera to color protein surfaces based on hydrophobic character. However, we have a color scheme which our lab has consistently used. In the switch from Chimera to ChimeraX, I have not found a way to color by hydrophobicity with our color scheme using this or other commands, but I have found a way to color hydrophobic regions onto surfaces, without the ability to change the colors. Is there a way to do this in ChimeraX? Thanks for the help! Best, _______________________________ Garrett Knotts Undergraduate Lab Assistant (Johnson Lab) Legislative Director of the Mississippi State University Student Association Vice President of Honors Ambassadors Sigma Phi Epsilon Learning Community Coordinator [cid:8783bc97-b3f7-4f42-85c5-130c16ad956f]

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Behavior of "cd" when executed through a script
by Vorländer,Matthias Kopano 29 May '24

29 May '24

Dear ChimeraX team, I have a series of scripts that contain a “cd” statement to set the working directory. I execute the scripts (which opens a model and map and colors the map). I then manually adjust the orientation and threshold and want to save a picture with “save map.png” (I want this png tp be saved in the folder that I set with the script). I have noticed that in this scenario ChimeraX has “forgotten” the cd statement from the script file and has fallen back to default working directory (or the last working directory manually set in the session before I exectuted my script). At least for me it would be more convenient and logical if the working directory can be set and maintained after habing executed a script. Note: if I don’t execute the script by double clicking but by copy/paste, the working directory is correctly maintained. Would be great if the behavior could be adjusted 😊 Many thanks and best wishes, Matthias

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Command not found from cxc file v1.7.1 on M2 Mac
by Hong Glenn Meng ZHAN 29 May '24

29 May '24

Evening all, I was trying to color code my imod models based on their volume (see attached). It worked ok for me just one model file opened in ChimeraX. When I was doing anther model file, I can passed the individual command in the command line to change color: color #1.1 #ceecc8 However, when I generate a cxc file and open it from command line or click on Open, it showed Unknown command: color #1.1 #ceecc8 Any input where I was not doing correctly? Thanks for helping! -Hong [Screenshot 2024-05-28 at 11.22.11 PM.png][image2.png]

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Python scripting for Dipole moment calculation
by andreumormaldon＠outlook.com 28 May '24

28 May '24

Hi all! I am trying to calculate the dipole moment of different proteins at different pH values. The .pdb and .dx files are generated with pdb2pqr and apbs software. I have found a script that is written for chimera, but it seems that the modules are not translated to ChimeraX, or at least I am not able to make it work. So I have decided to try to write my own script. So far I am able to obtain the center of mass of the protein as well as the charges of all the atoms in the molecule, but I cannot find a way to build a vector to where calculate the dipole (as it is done in the chimera script). Can anyone give me some insights? Does ChimeraX have as well the class Vector and Point? Thank you very much for your help! Best, Andreu

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Is it possible to set attribute on chain via Python script?
by Artie Kushner 28 May '24

28 May '24

I apologize in advance if this is off topic. I heard that people use chimerax mailing list to share tips and ask for help and saw some archives online that came in handy. I'm wondering if it's possible to set an attribute on the whole atomic chain (for future byattribute coloring) the way it is done in the example with Atom/Residue ? ( https://rbvi.github.io/chimerax-recipes/helixmlp/helixmlp.html) I'm trying something similar in my script: ``` from chimerax.core.commands import run from chimerax.atomic import Residue, Atom, Chain # the regular Cmd setup.. c:Chain polyclass:str = ... input from external spruce c.polymer_class = polyclass Chain.register_attr(session, 'polymer_class', 'Polymer Class', attr_type = str) ``` But when i run `color byattribute polymer_class /6 palette lipophilicity` it's not getting picked up: `No known/registered numeric attribute polymer_class`. Maybe it's not possible to color by string attributes? Thanks a lot for your advice Artem

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Morph Trajectory to smooth motion
by Alexander Hung Lee 26 May '24

26 May '24

I've morphed between a series of models/submodels to create a smooth trajectory but is it possible to morph a loaded trajectory that's topology and trajectory file (.nc)? Or is there another way to smooth the motion of it if morph is just to create a trajectory between models? Alex Lee PhD Student Woods Research Group<https://woodsgroup.franklinresearch.uga.edu/> Department of Biochemistry & Molecular Biology Complex Carbohydrate Research Center University of Georgia 315 Riverbend Rd. Athens, GA 30602 Email: ahl63010(a)uga.edu Mobile: (470) 641-3884

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Surface caps not drawn in script
by Daniel Asarnow 25 May '24

25 May '24

Hi Tom/Elaine, I have a series of models with SES surfaces and per-model clipping, and I am trying to create figures for each in a script with several blocks like the following: hide target m show #1 target ms save fig1.png If I run the commands myself, the figures are as expected, but when I run the script / copy and paste several of these blocks, the surface caps aren't drawn. Am I missing something? Or can I trigger the caps somehow? Thanks! Best, -da

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Re: Reg. alphafold contacts maxPae parsing
by Greg Couch 24 May '24

24 May '24

HI Anthony, Please send all ChimeraX question to the chimerax-users mailing list, so the appropriate person can answer you. While in general I am not involved with the alphafold support, in this particular case, I believe the answer is to use the current ChimeraX release candidate or daily build. Alphafold 3 changed the PAE format, so new code had to be written. And that has been mentioned on the mailing list, so if you are not already a member, I recommend joining. -- Greg On 5/24/2024 6:24 AM, Antony Merlin Jose wrote: > Dear Greg, > I have been using the alphafold contacts to parse the .pkl files to > show the pseudobonds in ChimeraX (e.g., alphafold contacts #1/A to > #1/B maxPae 5 distance 6). The .pkl files were generated from a > locally installed Alphafold 2.3. Now that there is an AlphaFold 3 > server, (https://golgi.sandbox.google.com/) I ran some complexes on > there and downloaded the results. The results include .json files that > have the PAE information. Would using the same commands with this file > also result in the correct parsing of the PAE values? How can I see > the python code that corresponds to each command on ChimeraX? > Thank you > Best, > Antony >

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