June 2019 - Chimera-users - RBVI Mailing Lists

Chimera - can I tweak the red color on the Red-cyan stereo view
by Tweten, Rodney K. (HSC) 11 Jun '19

11 Jun '19

We are displaying our protein structures on a large TV in the Red-Cyan stereo view, which works pretty good for 3D viewing (except the required loss of specific colors). We tend to see a bit of ghosting of the red structure, which I suspect is that the red color lens of the Red-Cyan glasses we have (we’ve tried a few with the same results) is not quite matched to that being used by Chimera in its Red-Cyan stereo view. I was wondering if there is any way the user could tweak the red color being used by chimera in this stereo view to more closely match that of the glasses (assuming that this is responsible for the ghosting of the red structure). Thanks! Rodney Tweten George Lynn Cross 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 FAX: 405 271-3117 Skype: toxlab1

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APBS
by Karl R Voigtritter 11 Jun '19

11 Jun '19

Hello, I am trying to display an APBS surface. I loaded a .pqr file that was generated using the http://nbcr-222.ucsd.edu/pdb2pqr_2.1.1 server. I then ran the APBS tool in the surface/binding analysis tab in Chimera. I left everything to default and clicked OK. It launched the executable and then executed it. The newly generated files came into the Surface Color window correctly. Upon trying to color the surface with the "color" nothing happens. -Karl Voigtritter, Ph.D. California State University, Chico

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Regarding MD simulation
by Divakar S 11 Jun '19

11 Jun '19

Hi, I have been trying to do MD simulation in chimera. However, i could not understand the exact procedure from the user help menu. Plz give us a detailed procedure for simulation and analysis if possible. I also tried to learn the procedures from previously published papers but i couldn't find any articles using MD simulation from chimera. Thank you -- *Dr. Divakar S, M. Pharm (Pharmacology), PhD.,* *Lecturer, **Department of Pharmacology,* *JSS College of Pharmacy,* *(A Constitute College of JSS Academy of Higher Education and Research, Mysuru)* *Ooty, The Nilgris, Tamilnadu.* *Mobile: +91-9944036345* *Email: divakar.s(a)jssuni.edu.in <divakar.s(a)jssuni.edu.in>, diva.niru(a)gmail.com <diva.niru(a)gmail.com>*

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viewing same size atoms within multiple molecules
by Andrew Garven 10 Jun '19

10 Jun '19

Hi, I am trying to implement a script so that each individual atom in each molecule I view on chimera is the same size (ie each carbon atom i view, regardless of the size of the molecule views a the same size). I realize this must be a function of the scale factor which changes the size of the molecules to appropriate viewing size. Is there a way to properly scale each molecule so that they have a standard atom viewing size. I would appreciate any help in this regard. Andrew

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voxel coordinates
by Andrew Garven 07 Jun '19

07 Jun '19

Hi I am trying to get a voxel encodings (coordinates) of molecules that are run through Chimera, as a deep learning model will have an easier time with such data. I am unsure how to retrieve such data from chimera. Any help would be greatly appreciated Andrew

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Re: [Chimera-users] THANKS! Chimera question
by Mike de la Flor 06 Jun '19

06 Jun '19

Hello, Thank you to all of you for getting back to me so fast. Thanks for the help. I am looking forward to ChimeraX Best, Mike de la Flor, CMI Board Certified Medical Illustrator PhD Candidate Biology and Biochemistry Natural Sciences and Mathematics University of Houston From: Greg Couch [mailto:gregc@cgl.ucsf.edu] Sent: Thursday, June 06, 2019 1:28 AM To: Mike de la Flor; UCSF Chimera users mailing list Subject: Re: [Chimera-users] Chimera question 1f16 is a NMR structure and as such has 20 different variations of the structure. Using the command line, you can hide all except for the first structure with the command: ~modeldisplay #0.2-20. To do that graphically, bring up the Model Panel, then click on the group/ungroup button to show controls for the individual structures. Then select the structures you don't want (click, drag, control-click, and shift-click as appropriate), and click on the hide button to leave the one you want. HTH, Greg On 6/5/2019 8:44 PM, Mike de la Flor wrote: Hello Mr. Pettersen, I apologize for bothering you but I had a Chimera question that is best explained by the screenshot attached. For some reason Chimera is importing multiple copies of 1f16.pdb. PyMol does not do this, but I prefer to use Chimera. Do you have any suggestions as to how to fix this? Thank you in advance. Mike de la Flor, CMI Board Certified Medical Illustrator PhD Candidate Biology and Biochemistry Natural Sciences and Mathematics University of Houston _______________________________________________ Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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Chimera question
by Mike de la Flor 06 Jun '19

06 Jun '19

Hello Mr. Pettersen, I apologize for bothering you but I had a Chimera question that is best explained by the screenshot attached. For some reason Chimera is importing multiple copies of 1f16.pdb. PyMol does not do this, but I prefer to use Chimera. Do you have any suggestions as to how to fix this? Thank you in advance. Mike de la Flor, CMI Board Certified Medical Illustrator PhD Candidate Biology and Biochemistry Natural Sciences and Mathematics University of Houston

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split map based on resolution or surface color
by Shu-Hao Liou 03 Jun '19

03 Jun '19

Hi Chimera User, Is that possible to split a density map base on its resolution? That means I have a surface color file contained all local resolution distribution through a density map. Best, Shu-hao

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