- ChimeraX-users - RBVI Mailing Lists

Manually imposed symmetry
by Shahid Khan 16 Sep '19

16 Sep '19

Hello I am having difficulty in manually imposing symmetry on a map (*.mrc file) and then extracting the unit cell for the subsequent fitting of PDB structures with fitmap. (1) When I use the command "Volume symmetry #1, C33 axis z centerIndex 107.5" I get the error message "No placements for #1" that I do not understand. (2) I cannot figure out from the help documentation on how to save and display one of the created segments. Any ideas? Thanks Shahid -- Dr Shahid Khan Senior Scientist Molecular Biology Consortium Lawrence Berkeley National Laboratory

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render buriedArea surface?
by Alexis Rohou 09 Sep '19

09 Sep '19

Hi all, I would like to depict the buried surface area between two chains. I have used "measure buriedarea" to measure it, and I can use "surface" to display the surfaces of either set of atoms, but I'd like to depict the surface of one of the chains, highlighting the region buried by the other chain. Is there a way to do this in ChimeraX? If not, does anyone have a recommendation as to how to achieve this? Perhaps by pre-computing the surfaces in another program? Thanks in advance! Cheers, Alexis

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vdw representation in chimeraX
by Elena Zehr 09 Sep '19

09 Sep '19

Hello, In chimera one can display dot van der Waals surfaces for atoms. *vdw* *atom-spec* <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html> What would be the equivalent command in ChimeraX? Thank you, Elena

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Open days EPFL - ChimeraX VR
by Krapp Lucien Fabrice 05 Sep '19

05 Sep '19

Hello, We are creating some small VR demos in ChimeraX for the EPFL open days in a few weeks (https://www.epfl.ch/campus/events/celebration-en/portes-ouvertes/) It is an event to show to a broader audience what the university is doing. The demos consists of small proteins up to density maps of bacteriophage with a few simple animations and menus to interact with the structures. Everything is almost done, I'm currently trying to fix the last issue but I didn't find a solution in the documentation. For two of the demos we would like the user to move a selection in VR with one of the VR controller right out of the box without having to go in the VR menu and click on the "move selected" button. I was able to make it work on Linux by loading the session though the remote API with the right part selected but it doesn't seem to work on Windows. The log shows a status change when clicking on the button "move selected" in VR but not the actual command to change the mode. Do you know if there is a way to change the mode of the VR controller without having to manually go through the menu in VR ? In the mean time, I will try different saved sessions and (remote) commands to try and solve the issue. If the demos are a success we will most likely make them available online so that anybody can try and improve them. Thank you in advance for your help. best, Lucien

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semitransparent volumes with ambient occlusion
by Sindelar, Charles 03 Sep '19

03 Sep '19

Dear Elaine, Eric, Tom, and team, I am happy to see ChimeraX is continuing to move forward! Here is a little request. For the figures that I am now making for publications, I have a special interest in showing semitransparent molecular maps together with the corresponding models, with ambient occlusion lighting on. I think ambient occlusion makes this kind of figure much easier to interpret and more beautiful. What I have noticed is ambient occlusion seems to get automatically turned off as soon as a map becomes less than 100% opaque. I always assumed this was due to some kind of rendering difficulty. But then, I noticed that sometimes I can “trick” an old version of ChimeraX to do exactly what I want! Below is an example. Basically, in ChimeraX 0.6 I can set up everything just the way I want with an opaque map, then turn down the map opacity and get a nice, pretty figure just the way I like it. But then, as soon as I show/hide anything in the Model Panel, the ambient feature gets turned off! I noticed that in the most recent daily build, this “trick” no longer works and I can’t seem to ever get the pretty combination of transparent maps and ambient occlusion lighting that I like. I sure would like to have this option! I guess there must be some reason it is disabled? Best, Chuck Sindelar Opaque map + PDB (ChimX v0.6) (pretty but the PDB is obscured) [cid:image001.png@01D55FF9.D8266CF0] After adjust to 80% map opacity (ChimX v0.6) (pretty!) [cid:image002.png@01D55FF9.D8266CF0] After unshow/show PDB model (ChimX v0.6) (argh!) [cid:image003.png@01D55FF9.D8266CF0]

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silhouette of transparent density
by YAO HE 30 Aug '19

30 Aug '19

Hi, I am using ChimeraX now to show the overlay between atomic model and transparent EM densities. However, when I enable the silhouette feature, only the transparent EM densities are affected. I am wondering if it is possible to also silhouette the atomic model inside. Just like "setattr M silhouette true #3" in Chimera. Best, Yao

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silhouette of transparent density
by heyao 30 Aug '19

30 Aug '19

Hi, I am using ChimeraX now to show the overlay between atomic model and transparent EM densities. However, when I enable the silhouette feature, only the transparent EM densities are affected. I am wondering if it is possible to also silhouette the atomic model inside. Just like "setattr M silhouette true #3" in Chimera. Best, Yao

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Chimera X and the Oculus Quest
by Thomas Gluick 28 Aug '19

28 Aug '19

HI First please excuse my computer language ignorance. My question is: Is the Oculus Quest compatible with Chimera X; if it is, is software available to link the program to the Quest. I am aware already that the Rift can be connected and also certain phones. Thank you for you time. Best Tom Dr. Thomas Gluick Assistant Professor of Chemistry School of Science and Technology 770-842-5532

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Question about Calphas and line between them
by Yazan Abbas 21 Aug '19

21 Aug '19

Hi, While looking through the user guide, I came across an option to draw a line between consecutive Calphas that are displayed. I made a mental note to use that option in my figure, but I failed to bookmark it or write down what the command was. I've been through the user guide several times again, but can't seem to find it. Would appreciate it if someone could jog my memory. Thanks, Yazan

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discontinuous helices in tube mode
by Yazan Abbas 19 Aug '19

19 Aug '19

Hi, Is there a parameter that can be changed to control how "cartoon style modeH tube" draws a continuous helix? In my model, most of my helices are broken up into 2-4 discontinuous helices (especially the long, curved ones). In pymol (cylinders mode) and chimera (pipes and planks depiction), the same helices are drawn as a single, continuous helix, suggesting that my model is ok. I tried adding a HELIX definition in the pdb file, and also tried forcing chimeraX to draw a helix using the setattr command, but neither strategy has helped. I also tried playing with the dssp energyCutoff with no success. Thanks, Yazan

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