April 2022 - ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] [Chimera-users] Chimera X color by attribute middle range value
by Elaine Meng 12 Apr '22

12 Apr '22

Hi Marcell! In ChimeraX, you can control which colors go with which values in the "palette" option of the "color byattribute" command. This option can take color/value pairs, and the "range" option is not needed in your situation (if I understand correctly). As you found, if you only give the range, it will spread out the colors evenly. Here's an example of value,color pairs if you want to color by attribute named "blah" using dodger blue for 0.2, red for 1.0, and gold for 4.0: color byattr blah palette 0.2,dodgerblue:1.0,red:4.0,gold <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#byattribute> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#palette-options> There are lots of named colors, although you could use hex codes instead if the named ones aren't quite what you want. <https://rbvi.ucsf.edu/chimerax/docs/user/commands/colornames.html> ChimeraX does not yet have a color-by-attribute GUI although that is something we would like to have eventually. The Color Key tool is just for drawing a color key to explain the coloring, but does not itself affect the structure coloring. By the way, you may be interested in the chimerax-users(a)cgl.ucsf.edu mailing list (CC'd on this reply) for questions/discussion specifically about ChimeraX. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Apr 11, 2022, at 5:07 PM, Zimanyi, Marcell via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello Chimera Community, > > I have a .defattr file where I have assigned a value to a few residues on my protein. I'd like to set the range to be 0.2, 1, and 4 so that values with 1.0 will be the middle color. I currently don't see a way to set the middle value for the range. In Chimera, I could set the middle range value in the define attribute GUI. In Chimera X, I'm using color byattribute range 0.2,4 because the range argument will only accept two values. I see that I can bring up the color key gui, but when I change the color key I don't see a way to update the coloring on the residues themselves. > > Could you please help me figure out how to set attribute range with 3 values as in Chimera? > > Thanks, > Marcell

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Command line disappared
by mhc128＠student.bham.ac.uk 12 Apr '22

12 Apr '22

Hello, I am currently completing a project requiring use of ChimeraX. I'm new to the program, and somehow the command line itself has disappeared for me. I have looked throughout the help section but could not find anything specific on re-enabling the use of the command line. Is there anything I am missing? Thanks for your time.

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Setting the same sdLevel threshold for several volumes
by Moisés Maestro López 11 Apr '22

11 Apr '22

Good morning, I would like to set the threshold of multiple CryoEM Volumes (10-20) at the same time, and I would like to put all of them at the same sdlevel. I use the command: volume #1 sdLevel 2 But this only work for one volume, if I use volume all sdLevel 2, or volume #1 #2 #3 sdLevel 2 It does not work and the threshold are random. In chimera I had a script that I use for doing that but I have not found the way to do it in ChimeraX. In Chimera, I normally called the script with an alias. alias ^allsd runscript ~/chimeraScriptSD.py allsd 3 And the script (chimeraScriptSD.py) was: import sys import chimera from VolumeViewer import Volume mlist = chimera.openModels.list(modelTypes=[Volume]) sdlevel = 2 if len(sys.argv)>1: sdlevel = sys.argv[1] for m in mlist: chimera.runCommand('volume '+str(m)+' sdlevel '+ str(sdlevel)) But I do not know how to do this in ChimeraX. The key point I do not know how to do is to do a loop that say “for any volume in all the opened volumes”. Thanks for your help Moisés

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Dependency trouble
by William Hofsøy 08 Apr '22

08 Apr '22

Hi, I was attempting to install my chimerax bundle on a different computer and encountered the error: No module named 'PyQt5' So I added this line to the bundle_info.xml under the Dependencies tag: <Dependency name="PyQt5"/> But I still get the same error?

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Re: [chimerax-users] [Chimera-users] Openning XYZ files with ChimeraX
by Elaine Meng 07 Apr '22

07 Apr '22

> On Apr 7, 2022, at 5:29 PM, Henrique Castro via Chimera-users <chimera-users(a)cgl.ucsf.edu> wrote: > > Hello, everyone, > I'm trying to adapt to ChimeraX and when trying to open an XYZ file I'm receiving the message "Opener for format 'XYZ file' is not installed; see log for more info". Is it possible to work with his format as in the Classic Chimera? > -- > Henrique C. S. Junior Hi Henrique, The message said to look at the Log, where it says: Install the SEQCROW bundle to open "XYZ file" format files. ... and "Install the SEQCROW bundle" is even a link that you can click to go directly to the SEQCROW installation page. So try installing that (which is easy, just click "Install") and then try opening your XYZ file. By the way, for asking questions about ChimeraX specifically, we recommend using the address chimerax-users(a)cgl.ucsf.edu (CC'd on this message). Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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wynton --nogui : how to use cd command ?
by Rangarajan, Amith 06 Apr '22

06 Apr '22

Hello everyone, i am new to using chimerax in --no gui mode $ chimerax --nogui UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. cmd> pwd Executing: pwd Current working directory is: /wynton/home/jacobson/avranga1008 cmd> cd /wynton/scratch/avranga1008/0-binana/0-docked-poses cd /wynton/scratch/avranga1008/0-binana/0-docked-poses ...^ Expected name of a folder to open/read; a name of 'browse' will bring up a file browser or a keyword please share your thoughts on how to change dir in the no gui mode. thanks, amith

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measure neighboring distance of histidine side chain
by HONG ZHAN 05 Apr '22

05 Apr '22

Dear all, I am interested to get a list of distances between histidine residues in my built model. Because I would like to see which crosslinker can potentially help to maintain the structure better during purification. I have noticed that I can measure one residue in chain A to all other atoms in chain B using contact function, however, I want to get a list of distances between any histidine imidazole (neighboring distance), is there a way to do that in ChimeraX? Super thanks in advance. Best, Hong

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display options for model with 2 chains
by Mauricio Losilla 05 Apr '22

05 Apr '22

Hi, I am new to ChimeraX, thank you for making this great software available. I loaded a pdb file that has 2 amino acid chains aligned (chimerax.png). These chains are a model (gray) and template (purple). As you can see, the two chains look weaved or blended. I would much prefer to display the uninterrupted template around to model, to visually represent their fit. Is there a way to do this? I am attaching a second image (ideal_display.png, generated elsewhere) with the visual outcome I am after (the purple chain is the template, the rainbow-colored chain is the model). Thank you *Mauricio Losilla, PhD* Integrative Biology; and Ecology, Evolution, & Behavior Michigan State University he, him, his

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Trouble with imports in ChimeraX bundle
by William Hofsøy 05 Apr '22

05 Apr '22

Hi, I have been doing some restructuring and refactoring of my project and started having trouble with my imports and modules not being found. previously all my imports were relative for instance: "from . import tool" However this is a bit impractical now that I have a folder structure, so I have been trying to use absolute imports like from "src.toolname.pythonfile import class" but it seems my folder structure differs from how it is after installing it into ChimeraX. I am using pycharm as my editor and the automatic import paths they set up also fails, meanwhile i looked at the sys.path and there the structure is chimerax/packagename where packagename contains the files contained in my src. So I was wondering if there is a way to set this up properly?

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Selection of the specific state from multi-model PDB
by Enrico Martinez 05 Apr '22

05 Apr '22

Dear ChimeraX users! Working in ChimeraX with multi-model PDBs I may use the following command to close all states but not the first (1.1): close #1.2-end How could I keep only the desired state (e.g I would like to display only the state #1.5 and close others)? Many thanks in advance Cheers Enrico

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