August 2022 - ChimeraX-users - RBVI Mailing Lists

Imod map values
by HONG ZHAN 26 Aug '22

26 Aug '22

Dear all, It might be not a good question regarding chimeraX. I have a PEET generated averaged map and output of PEET is reversed vs. single particle maps. What is a good function to change the density of PEET output? I used newstack -multadd -1,0 function in imod, however it gave -137 level… Thanks! Hong

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3d-SNFG representation of glycans
by Varga Julia 26 Aug '22

26 Aug '22

Dear All, I am trying to visualize glycans in ChimeraX, however I cannot find the possibility to use either the 3D-SNFG, nor the filled planar representation. Am I overlooking something? Is there a possibility to do this? [image: image.png] Thank you very much! Best regards, Julia Varga

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Job or output file name when running Alphafold in ChimeraX?
by Rayees Mattoo 24 Aug '22

24 Aug '22

Hi, Is there a way to name the AlphaFold run job or the output file in ChimeraX? Best Rayees

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Segment Maps In ChimeraX
by Myers, Jonathan 23 Aug '22

23 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 23 Aug '22

23 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 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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ChimeraX-users August 2022