November 2020 - ChimeraX-users - RBVI Mailing Lists

tips on how to use the "bond rotation" right mouse tool
by M. Elizabeth Stroupe 19 Nov '20

19 Nov '20

Hi all, I am working on a little side project to use ChimeraX with high school students to explore protein structures. I am looking for tips on how to make the program as intuitive as possible! I can't seem to make the "bond rotation" tool work easily. I gather you should be able to just highlight that, depress the right button, and move the mouse over the bond you want to move. Sometimes it works and sometimes it doesn't. What am I doing wrong? (and other tips besides having students do some of your tutorials before starting the activity would be very welcome!) Thank you! Beth

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General question about MODELLER
by Moradkhan, Tiglath A 19 Nov '20

19 Nov '20

Hi I have a question about using MODELLER. I've built models of a protein that I'm currently studying and wanted to know if it's necessary to minimize regions of the protein that may have poor quality based on the QMEAN score. Or does MODELLER minimize these regions when building homology models? Thanks Tiglath

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question about lighting options
by Ryan Cammarota 18 Nov '20

18 Nov '20

Hi, I am wondering whether there is a simple way in ChimeraX to set one point (or atom) as a light source, which could allow for the shadows cast by the surrounding atoms to be visualized? Thanks for your help, Ryan

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sequential coloring of a range of residues
by Daniel Larsson 17 Nov '20

17 Nov '20

Hi, I have trouble coloring only a narrow range of residues (1-10) in one chain (P) of one model (#18). I've tried a few options: color sequential #18/P:1-10 This colors the entire chain P in rainbow colors (equivalent to atom selection #18/P). color sequential #18:1-10/P This colors _all_ residues of all chains in model #18 -- except of one chain which lacks residues 1-10. I also tried with the "rainbow" synonym. When this failed, I tried coloring according to the residue number: color byattribute r:number #18/P:1-10 This throws an error "Unknown/unregistered Residue attribute number", although number should be an attribute of residues according to this page: https://www.cgl.ucsf.edu/chimerax/docs/user/attributes.html#residue Am I doing something wrong? Is this feature not implemented yet? Is there a work-around? Regards, Daniel N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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Command development
by Eric Pettersen 17 Nov '20

17 Nov '20

For any developers that will be implementing their own commands, we have put up a page about the considerations to think about when deciding on the command name and syntax, here: Command Style Guide — ChimeraX 1.2 documentation <https://www.cgl.ucsf.edu/chimerax/docs/devel/command_style.html> --Eric Eric Pettersen UCSF Computer Graphics Lab

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Atom specifier of manually selected group
by André Graça 17 Nov '20

17 Nov '20

Hi, I was wondering if there is any command that allows to list the atom specifiers for manually selected atoms using the ctrl drag and drop method. If there is one, I did not manage to frame my question properly to find it in the documentation, and I would appreciate some guidance. Thank you, André Graça

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Default movie image directory
by Daniel Asarnow 15 Nov '20

15 Nov '20

Hi, What is the default image directory when rendering on a movie on OS X? ChimeraX crashed while I was rendering (due to running out of space) and it seems like the images are taking up a lot of space somewhere. Thanks, -da

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[new-map-options] Error when using the "subregion" option
by Arthur Ecoffet 13 Nov '20

13 Nov '20

Dear ChimeraX developers, When using the "subregion" option for different map-related functions (volume morph, volume copy) I encountered the following error : *ValueError: could not broadcast input array from shape (150,150,150) into shape (151,151,151)File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\map\volume.py", line 982, in writable_copy*g.array*[:,:,:] = self.region_matrix(r) *If you want to reproduce the error, I worked on EMDB22000 and I typed in the console : *volume copy #1 subregion 150,150,150,300,300,300 *alternatively *volume morph #1 #2 subregion 150,150,150,300,300,300 * raises the same error. I tried on two versions of ChimeraX (including the last stable from September) and got the same error twice. Would you have any idea how to solve this? Thanks very much, Best, Arthur

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ChimeraX
by Reed, Scott 13 Nov '20

13 Nov '20

Helo, I am interested in getting a copy of the ChimeraX GitHub repository. I have some python code running on chimera that I would like to update to ChimeraX. Thanks, Scott Scott Reed scott.reed(a)ucdenver.edu<mailto:scott.reed@ucdenver.edu> https://ucdenver.zoom.us/j/3152346473

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Selecting a webcam
by Lewandowski, Jozef 13 Nov '20

13 Nov '20

Hi, If I have multiple webcams installed on my laptop how would I select a specific webcam to use with the webcam command? Thanks, Józef

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ChimeraX-users November 2020