August 2022 - ChimeraX-users - RBVI Mailing Lists

Measure volume at multiple threshold levels not function
by Christian Tüting 22 Aug '22

22 Aug '22

Dear ChimeraX-Team, I have an issue with the volume measure tool. I would like to measure the volume at different thresholds. Using the gui mode, I can type the following: volume #1 level 1 measure volume #1 LOG: Enclosed volume for surface (#1.1) = 4.012e+06 volume #1 level 2 measure volume #1 LOG: Enclosed volume for surface (#1.1) = 2.144e+06 So this is functional in principle. But I would like to run this in no gui mode, so the commands are ";" seperated. But, even in gui mode, I got the following: (threshold was set to 1 before executing) volume #1 level 1; measure volume #1 LOG: Enclosed volume for surface (#1.1) = 4.012e+06 volume #1 level 2; measure volume #1 LOG: Enclosed volume for surface (#1.1) = 4.012e+06 So the threshold level is not applied, prior to the measurement of the volume. And this is the same in the no-gui mode. I would like to check the volume at 5 different levels, but I got always the same value when executing: "/usr/libexec/UCSF-ChimeraX-daily/bin/ChimeraX --nogui --cmd 'open cryosparc_P42_J241_002_volume_map_sharp.mrc; volume #1 level 0.5; measure volume #1.1; volume #1 level 0.5; measure volume #1.1; volume #1 level 0.5; measure volume #1.1; volume #1 level 1; measure volume #1.1; volume #1 level 1; measure volume #1.1; volume #1 level 1; measure volume #1.1; volume #1 level 1.5; measure volume #1.1; volume #1 level 1.5; measure volume #1.1; volume #1 level 1.5; measure volume #1.1; volume #1 level 2; measure volume #1.1; volume #1 level 2; measure volume #1.1; volume #1 level 2; measure volume #1.1; volume #1 level 2.5; measure volume #1.1; volume #1 level 2.5; measure volume #1.1; volume #1 level 2.5; measure volume #1.1' --exit" Is there any command, that the threshold level is somehow applied, and the measure volume is executed correctly? The problem is present in UCSF ChimeraX version: 1.4.dev202202240543 and UCSF ChimeraX version: 1.5.dev202207221833 Best Christian

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AlphaFold prediction of complex - results not downloaded
by Erik Werner 22 Aug '22

22 Aug '22

Ladies and Gentlemen, This weekend, I did an AlphaFold prediction run of the human Troponin complex (Troponin C, T and I, UniProt-Ids P63316, P45379, P19429, respectively) via a freshly installed ChimeraX (v 1.4)/Google Colab on macOS Catalina (10.15.7). It completed successfully after 8 hrs (see screenshot below) but I failed to locate the results. According to your tutorial (https://www.youtube.com/watch?v=6lXeCPuTePs and https://www.rbvi.ucsf.edu/chimerax/data/alphafold-dec2021/af_multimer.html) I was expecting the results in a Prediction#-folder within the Downloads folder, but ChimeraX had only saved the UniProt xml files there. Also, the notebook code indicated the download of a "results.zip" folder but that also cannot be found anywhere on the computer. What have I done wrong? Would I have to edit the notebook? Specify a folder, and where? And: can I still recover the results from Google Colab servers? I copied the notebook to my GoogleDrive but was unable to identify a run-id or anything specific to my run. I would really like to get this working as the prediction of complexes is such a fantastic resource! Many thanks for your help, Erik Werner, Berlin /--// //Dr. Erik Werner// //Paulstr. 36// //10557 Berlin// //Germany/

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Re: [chimerax-users] writing names of models as a text file
by Rangarajan, Amith 19 Aug '22

19 Aug '22

Dear Chimerax team, I want to access the names of the models in a individual chimerax session , i am not able to find a way to write them out as a txt file or to the log . please help me find a way to do this. thanks again for all your help, best amith

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Sym #1 command not executing
by John O'Brien 19 Aug '22

19 Aug '22

Hello, I am a new user to ChimeraX, and was doing the examples in the Quick Start Guide as practice. While following the Atomic Structure Commands, the "sym #1" command did not appear to produce the full table of symmetries, as described in the guide. Could you please help me with this? I have attached a screenshot of what I see to this email, hopefully that helps. Best, John O'Brien

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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 18 Aug '22

18 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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