- ChimeraX-users - RBVI Mailing Lists

Segment Maps In ChimeraX
by Myers, Jonathan 22 Aug '22

22 Aug '22

Dear ChimeraX User Group, I'm trying to segment a map using an atomic model as a reference. To make my life easier for many of the operations I use in my work, I centered all of my structures to the origin of the session. However, when I want to segment out parts of my density, the original coordinates of the map are used for the various regions. I, therefore, can't use my centered structures as a reference as I had originally planned. I don't know if this is a bug or if this is intentionally programmed, but I am having a difficult time re-aligning the segmentation to my origin-based coordinate system. Is there a better way to do what I am trying to do or am I out of luck? Thank you. Shosholoza, Jonathan Myers

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request for true transparency support in .bild files
by Francois Berenger 22 Aug '22

22 Aug '22

Dear chimera hackers, In the old Chimera (not X), if I put two transparent spheres in a .bild file: one sphere can completely hide the other (e.g. a small one inside of a bigger one). While, if there was true transparency, no sphere should completely hide another. Is this better handled in ChimeraX? I _love_ .bild files, because it is so easy to generate them in order to annotate a 3D molecular system then view all of it (molecules + annotations) in Chimera. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html Thanks a lot, F. PS: here is an example problematic .bild file for the old chimera --- .color green .transparency 0.750000 .sphere -0.542700 0.122500 -0.047867 1.500000 .sphere 1.060560 -1.270600 -0.236620 1.500000 .color orange .transparency 0.750000 .sphere 0.611100 -2.324200 -0.346200 1.250000 .sphere 1.108100 2.092000 0.140700 1.250000 .sphere -3.097400 0.651000 0.062700 1.250000 .color grey .transparency 0.750000 .sphere -0.542700 0.122500 -0.047867 1.500000 .sphere 1.060560 -1.270600 -0.236620 1.500000 .sphere -1.453700 2.784800 0.269900 1.500000 .sphere 3.272900 0.026100 -0.134900 1.500000 .sphere -2.354000 -1.959600 -0.245900 1.500000 ---

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Morph map parts transformation in a complex
by HONG ZHAN 22 Aug '22

22 Aug '22

Dear user group, I am trying to do volume morph to transform different parts of a complex into another part of the same complex. Because I did drag and fit each segmented parts, the map positions are no longer the same and I have this error: Map positions are not the same. Is there a way to do the map morph to transform different map parts in the complex? Many thanks! Hong

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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 18 Aug '22

18 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 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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