November 2020 - ChimeraX-users - RBVI Mailing Lists

Animation feature in ChimeraX?
by Eric Pettersen 21 Nov '20

21 Nov '20

> Begin forwarded message: > > From: "Tweten, Rodney K. (HSC)" <Rodney-Tweten(a)ouhsc.edu> > Subject: Animatin feature in ChimeraX? > Date: November 20, 2020 at 10:05:00 AM PST > To: "chimerax-users(a)cgl.ucsf.edu" <chimerax-users(a)cgl.ucsf.edu> > > > Hi, > I have used Chimera for years for my publications and for generating animations for lectures and invited talks. I found the animation feature incredibly easy to use and intuitive. However I did not find a similar feature in ChimerX. I read about the Morph command but to me this seems much more complicated to use and much less intuitive. Is there a graphical interface to the Morph command or is this going to remain a command line feature only? I often use the animation feature of chimera to morph between two structural states, which is really easy. > Cheers, > Rodney Tweten, Ph.D. > George Lynn Cross Professor > Presidential Professor > > "Anti-intellectualism has been a constant thread winding its way through our political and cultural life, nurtured by the false notion that democracy means that my ignorance is just as good as your knowledge.” > Isaac Asimov > > BMSB-1053 > 940 Stanton L. Young Blvd. > The University of Oklahoma Health Sciences Center > Oklahoma City OK 73104 > USA > Work phone: 405 271-1205 > Web page: https://basicsciences.ouhsc.edu/mi/Faculty-and-Staff/Primary-Faculty/rodney… <https://basicsciences.ouhsc.edu/mi/Faculty-and-Staff/Primary-Faculty/rodney…> > Skype: toxlab1

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ChimeraXClassifier platform attribute
by Daniel Esteban Palma Igor 21 Nov '20

21 Nov '20

Hi, I have a command that will work in mac and linux but not in windows, Should I create a separate ChimeraXClassifier for linux and mac with the corresponding platform attribute or there is a way to create only one ChimeraXClassifier for both? Regards, Daniel Palma Igor

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Transparency for atoms selected only
by Gabriele Cerutti 21 Nov '20

21 Nov '20

Hello, I am trying to display transparency only for selected residues in my protein model but I am having a hard time trying to restrict the transparency only to the selected set of atoms (it sets the transparency to all residues). Do you have any suggestions and/or examples about this? Thanks, Gabriele

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Saving biomt record for generated icosahedral
by Moustafa, Ibrahim M. 20 Nov '20

20 Nov '20

Hi all, I built a full icosahedral model from ASU in chimeraX, how can I save the coordinates and BIOMT record of the generated full-model? Thanks for helping. Ibrahim

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Re: [chimerax-users] [Chimera-users] color by zone in chimeraX
by Elaine Meng 20 Nov '20

20 Nov '20

Hi Pranav, I’m Cc'ing the chimerax-users(a)cgl.ucsf.edu list (recommended for ChimeraX questions). I believe the problem is that when coloring the chains you are using “target c” which means to color only cartoons, whereas coloring by zone uses the atom colors. Since you only colored the cartoons, the atoms probably still had heteroatom color-coding. If you use “target ac” instead (even if the atoms aren’t shown), then as long as the color zone distance is big enough, I think you will get the color zones you expect. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#simple> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#zone> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > On Aug 20, 2019, at 10:54 AM, Pranav Shah <p.shah.lab(a)gmail.com> wrote: > > Hi Elaine and Co., > > I am trying to color a virus map with the relevant pdb file, the > series of commands I am running are as follows, > open virus.mrc > open virus.pdb > color /A plum target c > color /B lightgreen target c > color /C dodger blue target c > color zone #1 near #2 dist 3 > However, the resultant surface is rendered in splotches of red and > blue, which leads me to think the it is coloring the surface using > atom type. Could you tell me how I can get Chimera X to color the > surface using the colors of the chains only? FYI, color by zone works > flawlessly in chimera. > > Cheers, > Pranav

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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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