August 2022 - ChimeraX-users - RBVI Mailing Lists

Moving/aligning/ modifying the model
by Dmitry Semchonok 30 Aug '22

30 Aug '22

Dear colleagues, Is there a way I can move(rotate) the chain/residue within a model in ChimeraX? If yes, then how? Thank you in advance. Kind regards, Dmitry

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Zooming into the areas on click
by Dmitry Semchonok 29 Aug '22

29 Aug '22

Dear colleague, For presentation purposes: I would like to show the full map/model structure, then I would like to zoom in on particular areas: area 1, then area 2, then…. (preferably in motion). How is it possible to do in chimeraX? Probably as a movie? How? Thanks in advance! Kind regards, Dmitry

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Can I change the curved cylinder into a straight one?
by 王超(Chao Wang) 28 Aug '22

28 Aug '22

Dear All,After displaying helix in cylinder mode, I found that it is curved by default. I would like to ask whether it can be changed to a straight shape with two ends as fulcrums or other straight way?Thanks,Chao.

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Questions on job status
by Will Grubbe 26 Aug '22

26 Aug '22

Hello, I've submitted a few jobs using ChimeraX and am wondering how to check the status of them. I just need to fill in a few residues in a protein complex with known sequence - where can I find the results when they are done? Thank you for your help, Will

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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 23 Aug '22

23 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 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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