- ChimeraX-users - RBVI Mailing Lists

downtime on Monday, December 7, 2020
by Elaine Meng 03 Dec '20

03 Dec '20

Dear Chimera and ChimeraX users, We will be doing some system maintenance on Monday, December 7. During this downtime, which we expect to last one day, the Chimera and ChimeraX websites, downloads, e-mailing lists, and several web services accessed by the programs will not be available. Apologies for any inconviences this may cause, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

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Plugin developers switch from PyQt5 to PySide2
by Tom Goddard 02 Dec '20

02 Dec '20

For those who develop ChimeraX plugins with graphical user interfaces, today we switched ChimeraX from using PyQt5 to using PySide2. These are nearly identical Python interfaces to the Qt window toolkit. In your code you will probably only need to change imports of PyQt5 to instead import PySide2. There are a few other small differences (e.g. pyqtSignal becomes Signal, and QAction callbacks may not have the same arguments) and more details about the differences are in this ChimeraX ticket <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1635#comment:34>https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1635 <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1635> We made the switch because PySide2 has a bigger community development team, part of the Qt project, and has less restrictive licensing. Tom

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Add Chain to AtomicStructure
by Daniel Esteban Palma Igor 02 Dec '20

02 Dec '20

Hi, is there a way to add a Chain object to an AtomicStructure? Regards, Daniel Palma Igor

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BUG - NotADirectoryError when start Chimerax
by 江文宏 01 Dec '20

01 Dec '20

Hi, I am a phD from Peking University, Beijing, China. And I downloaded the latest version(1.1) of Chimerax for Centos. And I installed the chimerax in the linux (centos7) by yum install ucsf-chimerax-1.1-1.el7.x86_64. And everything went well for the install/compiling process. However, when I started the chimerax in the terminal, the terminal returned this error: Do you have any idea about such errors? I also tried the older version(1.0), but I got the same error. BTW, I used python3.8. Thanks! All the best, Wenhong Jiang

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New color picker alpha channel and custom color
by Daniel Asarnow 30 Nov '20

30 Nov '20

I noticed in a recent ChimeraX build the color picker has been simplified: [image: image.png] It seems we can still set the alpha channel within the "custom" color dialog, but the default color there is some shade of red regardless of the currently selected color. Could the custom dialog start at the current color by default? Setting the alpha channel via the picker is the fewest number of clicks, and starting at the current color will make slight adjustments much easier as well. Best, -da

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Problem with C2 symmetric assemblies
by Y. Mutum 30 Nov '20

30 Nov '20

Hi I have a a C2-symmetric pdb: 1be3 and have created a symmetric assembly using the command. >>> sym #1 assembly 2 newModel false The idea is to superimpose Chain /C of 1be3 and its symmetry partner with that of 3cx5 (corresponding chains -C and N) to get of deviations b/w the chains. However, when I try to 'match #1/C with #2/C, then I am getting only half of the C2 symmetric assembly superimposed. Is there a way to superimpose both of the chains-C of 1be3 to 3cx5? I could open the model 1be3 twice and then superimpose to the equivalent subunits (chains C and N) of 3cx5, one at a time. But the resulting superimposed assembly 1be3 (from 2 different models) is not going to be the C2 symmetric. In short, for 1be3: pdb, is it possible to rename the symmetry mate with different chains and get the C2 symmetric assembly as a single model? Say, for this new 1be3 C2-symetric assembly, you rename the second symmetry partners chains - Chain C as C1, Chain B as B1 for example in that new model. The idea is to have a C2 symmetric model with different chains, so that it can be compared with other models easily. Thanks Yaikhomba

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User defined color values for each residue/position
by Niccolò Arecco 30 Nov '20

30 Nov '20

Hi, I’m using ChimeraX to visualise the structure of a complex of 4 proteins. I generated a sequence alignment of protein sequences of 1 of the 4 proteins and at each column (amino acid) of the multi protein alignment I assign a score from 0 to 1, where 0 represents no sequence conservation and 1 represent perfect sequence conservation. I’d like to colour-code these values on a publicly available structure. Can I do it with ChimeraX? I tried to google a bit and read the docs but couldn’t fine a way. The input “colouring” file could be something like this tab delimited file: #POS AA SCORE 1 M 0.2 2 V 0.5 …. n N 0.8 But I can reshape it in a better format if necessary. If this is not possible to do it with ChimeraX are you aware of any other tool / software that would allow me to do this? In the end I’d like to be able to do something like ConSurf (https://consurf.tau.ac.il <https://consurf.tau.ac.il/>) does but I’d like to avoid if possible always having to use the web interface as I’d like to semi-automatise this process for every protein in the complex at least. Thanks a lot! Best wishes Nicco

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Coloring pdb surface by different colors
by Y. Mutum 27 Nov '20

27 Nov '20

Hi I have a pdb with 10 TMH (single polypeptide protein, so only 1 chain in pdb). The first TMH are colored in green and the rest in yellow. Is there a way to create a surface that consists of both these colors? i.e. Surface corresponding to TMH's 1-5 is colored in green, while the surface corresponding to TMH's 6-10 in yellow? I tried the surface command option but it seems to color the entire surface in a uniform color. Any suggestions would be very helpful. Thanks Yaikhomba

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Measuring Angles in ChimeraX
by Y. Mutum 27 Nov '20

27 Nov '20

Hi I am trying to measure angles between three atoms using ChimeraX by typing >>> angle #1/a:1001@FE, #1/d:1001@FE,#1/a:141@C However, the log reports: angle #1/a:1001@FE, #1/d:1001@FE,#1/a:141@C Unknown command: angle #1/a:1001@FE, #1/d:1001@FE,#1/a:141@C I have also tried to check if 'angle' is a valid command in the ChimeraX window I have opened. >>>usage angle In Log ---> "angle" is not a command name However, angle does seem to be a valid command in ChimeraX. In the documentation here -- http://www.cgl.ucsf.edu/chimerax/docs/user/commands/angle.html. I am using ChimeraX-1.0 ( version: 1.0 (2020-06-04)) I might have missed things out - Could you please give an idea of how i could measure angles using the command line in ChimeraX? Thanks Yaikhomba

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Build DNA structure in Chimera X
by Andreas Göransson 27 Nov '20

27 Nov '20

Dear Chimera X users, I have recently switched to Chimera X from the previous version. Do anyone know if there still is a possibility to build DNA structures as in the previous versions of Chimera? THanks in advance, Andreas Best regards Andreas Göransson PhD Student ITN Linköping University Phone +46 11 36 30 79 Visiting address: Hus Kopparhammaren, G518, Campus Norrköping

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