August 2022 - ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] Question about Coulombic scale bar in ChimeraX
by Elaine Meng 18 Aug '22

18 Aug '22

Hi Guipeun, This is the usual situation: The Color Key is not saying that -10 to +10 are the entire range in your structure, it is just showing how the color changes between -10 and +10. You would not change the values on the color key unless you also change the coloring. Any areas of the surface that have values beyond the range just get the same color as that end of the Color Key. I.e., all surface points with values below -10 (all the way down to the minimum for your surface -13.11) are the pure red shown at one end of the Color Key, and all surface points with values above 10 (up to the maximum for your surface +21) are the pure blue color shown at the other end. In between -10 and +10 the color gradually changes, and showing that change is the purpose of the Color Key. The tutorial uses "coulombic" with the default coloring, and the "key true" option in that command shows the values for that default coloring which are red for -10, white for 0, and blue for 10. <https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#k…> If you used different value/color settings in the command, then the key would appear with those different settings. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. it is recommended to send questions to chimerax-users(a)cgl.ucsf.edu (CC'd here) unless you are including data that needs to remain private > On Aug 18, 2022, at 12:14 PM, Guipeun Kang <Guipeun.Kang(a)UTSouthwestern.edu> wrote: > > Dear Dr. Elaine Meng, > > My name is Guipeun Kang, a postdoctoral researcher in Dr. Ryan Hibbs at UT Southwestern medical center. > > I have a silly question about scale bar of Coulombic surface. > > I displayed Coulombic potential of 3eeb, which is an example on ChimeraX tutorial page. > https://www.rbvi.ucsf.edu/chimerax/features.html > > In the Log, Coulombic values are minimum -13.11 and maximum 20.86 for chain A, but the scale bar is ranged from -10 to 10 when I add color key as shown in the instructions. > https://www.rbvi.ucsf.edu/chimerax/docs/user/tutorials/binding-sites.html#k… > > My question is: > When I type command "coulombic protein key true", the range of Coulombic surface of 3eeb is automatically reflected from -10 to 10? Or, should I manually change the scale bar range from -13 to 21 as shown in Log? > > I'm attaching a screenshot of ChimeraX Log and Color Key panel related to my question. > > I really appreciate your help, > Guipeun > > <image.png> > > UT Southwestern > Medical Center > The future of medicine, today.

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How to get back to original view after running resfit
by Rayees Mattoo 17 Aug '22

17 Aug '22

Hi, I am using resfit command. Is there a command or way to go back to the original view? Best, Rayees

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Rotate image on screen by 6 degrees?
by Robert Stroud 15 Aug '22

15 Aug '22

Is there a command that would rotate the image on screen (model and em map) by 6 degrees around the y axis? Im trying to make crossed eye stereo image for a paper, so I can then put the two images together in illustrator - as I see it Chimerax does not do crossed eye stereo, - and in stereo mode the center of rotation is not in the center of the image for me, so that the half images appear windowed differently on left and right? Thank you Robert Stroud stroud(a)msg.ucsf.edu <mailto:stroud@msg.ucsf.edu> 415 987 7535

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command question
by Kwangjun Lee 15 Aug '22

15 Aug '22

Hello, How can I adjust the position of the distance label? I figured out how to adjust the label for the residues. Thanks!

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Alternative locations
by Michael Bruist 15 Aug '22

15 Aug '22

In a demonstration page for students, I wish to show how the presence of the 2’OH on a ribonucleotide creates a clash at the active site of DNA polymerase. We are also trying to see if 2’OH’s create clashes within the primer. I have created a PDB file with deoxyribose as alternative location A and ribose as alternative location B. This works in original Chimera, but I am not getting it to work in ChimeraX. I am not able to specify the alternative atoms by their A and B designations. I do not see alternative locations in the hierarchy under target specification in the documentation. My PDB file is attached. Residues 106-113 have alternate locations included. The command “altlocs change A :113" does not seem to change anything, nor does changing the selection buttons in the Altexplorer. Mike Bruist mbruist(a)sju.edu

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docked UI
by Pranav Shah 13 Aug '22

13 Aug '22

Hi Team, Is there a way to make sure that some UI elements (eg. the chimerax python console) that I have enabled by calling from a custom startup script are pinned into the main window instead of appearing as floating windows? Best, Pranav -- Pranav Shah Postdoctoral Research Fellow. Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

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ISOLDE download
by Jason Mears 12 Aug '22

12 Aug '22

I am trying to download the ISOLDE bundle for my ChimeraX software. I have been unsuccessful thus far. The download starts, but it never completes the download. I have tried a number of times and logged in using my university credentials thinking that this might help. Nothing yet. I am running OS Monterrey (v 12.5). Any advice is appreciated. Thanks. - Jason Mears -- Associate Professor of Pharmacology Graduate Program Director, Pharmacology Center for Mitochondrial Diseases Case Western Reserve Univ SOM 216-368-3348 jason.mears(a)case.edu <mears.jason(a)case.edu>

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Drag select blanks view window
by Daniel Asarnow 09 Aug '22

09 Aug '22

In ChimeraX 1.3 and now 1.4 releases, I have an issue where control-click dragging to select causes the 3D viewer frame to black out. Everything else functions normally, including the select itself, although it is very difficult to use since the structure can't be seen. The select box *is* visible, but it's magenta instead of green. Afterwards things go back to normal if something was box selected, but if nothing was boxed then the 3D viewer remains blacked out until an interaction like moving the models/camera takes place. I'm on a 2021 M1 MacBook Pro with macOS 12.4. I was wondering if others have experienced this and if it's an M1 issue as this is the only machine I've seen exhibit the problem. Best, -da

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Distance between two residues
by Kwangjun Lee 07 Aug '22

07 Aug '22

Hello, Do you have a command that measures the distance between two residues? For example, I have a dimer model, and I want to measure the distance between /A:100 and /B:200 Thanks! Kwangjun Lee Ph.D. Candidate Department of Biomedical Sciences Florida State University College of Medicine 1115 W. Call Street Tallahassee, FL 32306 Tel: (850) 491-6985 Email: kwangjun.lee(a)med.fsu.edu<mailto:hyojeong.yong@med.fsu.edu>

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maps not on same grid in new ChimeraX?
by Moritz, Michelle 05 Aug '22

05 Aug '22

Hello, I recently updated my ChimeraX to version1.4(2022-06-03). It seems that now when I open cryoEM maps they are not always opening on the same grid, although they have the same box and pixel size. As I recall, in previous versions of Chimera, maps with the same box and pixel size would open in a coordinated, overlapping fashion, and they would move together when manipulated. Is there a preference that I need to set in the latest version in order for this to happen? Thanks for your help, Michelle

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ChimeraX-users August 2022