September 2019 - Chimera-users - RBVI Mailing Lists

calculating virus surface in prep for radial color display
by Gampe, Robert 23 Sep '19

23 Sep '19

Hi Chimera Users This is 2nd send to you after I enrolled as a CHIMERA user :), thanks. I need to calculate a radial distance plot from a surface representation of an Adeno Associated Virus structure as shown from literature below. However the: 1. Action, Surface, Show command fails, reporting CHIMERA often fails for large structures ( AAV is easily over 200K atoms ) with multiple chain IDs ( I have 60 individual chain IDs for each of the 60 capsid proteins ). Other CHIMERA popup suggestions did not resolve the problem either ( changing molecular surface parameters in the Inspect Selection ( actually didn't see anything to change ) or in PREFERENCES - NEW SURFACES. I tried using CHIMERA, Structure editing, change chain IDs to all chain A, but that was disallowed. Summary: could not figure out how to get CHIMERA to calculate and display a surface representation of an AAV virus and then use that display to calculate radial coloring as shown below. Any solutions greatly appreciated and thanks. Rob [cid:image001.jpg@01D56FEE.1FF9C5A0][cid:image002.jpg@01D56FEE.1FF9C5A0] _________________________ Robert Gampe, MS | Senior Scientist | RDRU Structural Biology| Pfizer Inc. 7030 Kit Creek Rd, Morrisville, NC 27560 Office: 919-666-5969| Robert.Gampe(a)pfizer.com<mailto:Robert.Gampe@pfizer.com> [cid:image006.jpg@01D4D043.EB786830] _________________________

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(no subject)
by Susy López 23 Sep '19

23 Sep '19

Dear all I am starting to use Chimera as a master's student and I have some difficulties. I know how to select the amino acids that are part of the surface of my protein. However, I don't know how to select the atoms of the surface. Specifically, the atoms accessible to the solvent. My second question is: I would like to know how polar amino acids (arginine, asparagine, aspartic acid, cysteine, etc.) and non-polar amino acids (alanine, glycine, isoleucine, leucine, etc.) can appear. Is there any configuration that allows me to identify polar and non-polar amino acids for edit them? Is it possible to customize those amino acids when I select them? I would be grateful if someone could help me, thank you. Best regards, Susanna

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Chimera laptop features required
by Aron Singletary 19 Sep '19

19 Sep '19

I was looking for system specs and ran across this comment: "I don't think you can buy one anymore, but the best laptops were those with NVIDIA Quadro (not NVS) graphics and a 3D stereo display (120Mhz, 3D glasses). Chimera needs workstation graphics (NVIDIA Quadro or AMD FirePro/FireGL), to support 3D stereo viewing." Just wanted to let you know there are still many great systems available with Quadro and FirePro graphics, they will usually be a good bit more expensive than traditional consumer laptops though. Our older GoBOXX SLM available in 15" with the Quadro P3200. https://www.boxx.com/systems/mobile-workstations/goboxx-slm/goboxx-slm-vr Our newer GoBOXX SLM available in 15" or 17" with Quadro RTX300-, RTX4000 or RTX5000. https://www.boxx.com/systems/mobile-workstations/goboxx-slm/goboxx-slm-15 Or if you are looking for a true desktop replacement we have our GoBOXX MXL. https://www.boxx.com/systems/mobile-workstations/goboxx-mxl Thank you, Aron Singletary Enterprise Representative BOXX Technologies 10435 Burnet Road, Austin, TX 78758 Work: (512) 852-3347 Toll Free: (877)877-2699 x347 Fax: (512) 835-0434 Email: asingletary(a)boxx.com<mailto:asingletary@boxx.com> www.boxx.com<http://www.boxx.com/> [BOXX_Logo_email]

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Fwd: chimera install problem
by Elaine Meng 18 Sep '19

18 Sep '19

Oh sorry, I was waiting for someone else to answer because I didn’t realize until now that you sent this message to only me. I don’t know anything about this subject, so I’m forwarding your message to the chimera-users mailing list for somebody else to reply. We recommend sending Chimera questions to this list instead of to individual developers. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco > Begin forwarded message: > > From: 陈柳青 <519198561(a)163.com> > Subject: chimera install problem > Date: September 17, 2019 at 5:31:06 AM PDT > To: meng(a)cgl.ucsf.edu > > Hi! > I have a problem when install chimera-1.13.1-linux_x86_64.bin <http://www.cgl.ucsf.edu/chimera/cgi-bin/secure/chimera-get.py?file=linux_x8…> in my computer, its opensuse system. > can you tell me how to solve this problem? as i am not familiar with linux system. > sincerely! > Liuqing Chen > >

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Chimera inquiry
by Danny Turin 18 Sep '19

18 Sep '19

Dear Sirs and Madames, I first want to start by sharing my appreciation with you for creating this program. It has been very helpful in my biochemistry course. I have been using the program to compute the total area and volume. Is there a way to only select either the polar or non-polar residue in the surface structure to determine volume and area. Thank you for your time. Sincerely, *--Daniel Turin * University of Minnesota Class of 2021, B.S. Health Sciences l turin005(a)umn.edu l (651)-600-0805 l

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Unable to Find Function
by Bailey Onken 17 Sep '19

17 Sep '19

Hello, I am currently a student in Biochemistry. I have a protein and I am trying to separate polar and nonpolar residues located on the surface of these molecules and then finding the values for the surface area associated with polar and nonpolar areas. If you can help me get to this function I would be very grateful. Thank you very much, Bailey -- *Bailey Onken *| Student, University of Minnesota Rochester 507.329.7409 | onken031(a)umn.edu

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How to draw 3-fold axis of a Icosahedron
by sunyeping 17 Sep '19

17 Sep '19

Dear everyone, I created an icoshedron with "Tool>high-order structre>Icoshedron surface" menu. Do you know how to draw 3-fold axis of a Icosahedron so that I can see the 3-fold symmetry center on the icoshedron surface? Thank you in advacne.

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Command line equivalence for Render by Attribute radii
by Sygusch Jurgen 16 Sep '19

16 Sep '19

Hello, I cannot seem to find the command line equivalence for Render by Attribute radii. I am trying to display a tunnel where the atom B-factors represent the tunnel radius. I am able to display the tunnel as expected by using the GUI. In the GUI, when I do Tools --> Depiction --> Render by Attribute --> atoms --> My Model; then Render Attribute --> bfactor; Radii --> Atom Style --> Sphere, I get the expected result of the tunnel diameter varying according to Bfactor (tunnel radius). What is the command line equivalence for doing this? I cannot seem to find it. Thank you for looking into this.

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Selecting residues with zones when reference is absent
by Carlos G. Oliver 16 Sep '19

16 Sep '19

Hello, I would like to select all ligands that are within a distance of nucleic acids but above a distance from proteins. The selection command I have so far is: `select nucleic acid z<10 & protein z>10 & ligand` This works for PDBs that contain both nucleic acids and protein. However, some will only contain nucleic acids, and in this case the `protein z>10` condition will result in an empty selection even when there is a valid ligand. I was wondering if there was a way to check whether the model contains protein to run a different selection command for each case, or to use a different selection command which handles both cases. Thanks! Carlos G. Oliver

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Dockprep OT2 C terminal question
by Danilo Boškovic 16 Sep '19

16 Sep '19

Dear caretakers, I have a non-standard residue OT2 (C terminus last O atom) that does not get recognized in the amber force field (everything else is fine). How do i rename this residue so it is properly accounted when adding charge? Sincerely, D. Boskovic

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Chimera-users September 2019