- ChimeraX-users - RBVI Mailing Lists

Re: [chimerax-users] [Chimera-users] ChimeraX and crosslinks visualization
by Elaine Meng 04 Sep '18

04 Sep '18

Hi Pascal, Many features are are still in development, so although we can easily imagine useful features (and we welcome your suggestions), many are not yet implemented. Yes, you can load different sets of crosslinks. The “pseudobond” input format is just plain text specifiying pairs of atoms. <http://rbvi.ucsf.edu/chimerax/docs/user/pseudobonds.html> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#atomic> Then you can specify the different models (input file -> model) in the “crosslinks histogram” command by their numbers as shown in the Models panel, e.g. crosslinks hist #1.3 crosslinks hist #3 <http://rbvi.ucsf.edu/chimerax/docs/user/commands/crosslinks.html#histogram> Currently there isn’t color-by-length or selection-by-length, sorry. The interaction with the histogram that you may already have seen is that passing the cursor over the columns of the histogram temporarily enlarges the corresponding-length pseudobonds and hides the others. There isn’t control over how wide the histogram bars are. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco P.S. there’s a chimerax-users mailing list CC’d on this message which you can send to and/or join > On Sep 1, 2018, at 2:57 AM, Pascal Albanese <pascal.albanese(a)polito.it> wrote: > > Dear Support Staff, > > first of all many thanks for developing Chimera! > > I'm using ChimeraX to integrate CryoEM and crosslinking MS data.I think that some features might be further implemented (or maybe are already there but i don't know how to use them): > > - Is it possible to load different sets of distances/crosslinks (like with different IDs)? > - is it possible to color code the distances with a cutoff (like red if >30 for instance)? > - The histogram and network is a nice feature, but it would be nice if there were some grouping based on the distances (i.e.: 1 to 5 A; 5 to 10 A, 10 to 15 A... etc), and then you can click on the column representing your distances class to select them (so you can make a subgroup, or delete them, or edit them etc...) > > that's it, maybe something can be done writing the code but unfortunately it's not my job. > > Thanks a lot and looking forward to hear from you, > > Cheers, > Pascal

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FYI: Model.id_string API change
by Eric Pettersen 22 Aug '18

22 Aug '18

For those of you writing code in ChimeraX, in case you’re using Model.id_string you should know that as of tomorrow’s build, Model.id_string is a property instead of a function. —Eric Eric Pettersen UCSF Computer Graphics Lab

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question about chimerax
by Fang, Fei 14 Aug '18

14 Aug '18

Hi, This is Fei from University of Pittsburgh. Here is a question about chimera x. By introducing two structures into the chimera x, how can I move the one structure over so that they're no longer covering each other? Thanks. Best, Fei

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Export a scene from Chimera and into ChimeraX?
by Oliver Clarke 06 Aug '18

06 Aug '18

Hi, I love the new visualization features in ChimeraX, but I also really like the depth of functionality available in the original Chimera. I understand that ChimeraX has been rebuilt from the ground up and therefore can’t be expected to support importing sessions from Chimera1. However, Chimera1 is also able to export static scenes - e.g. as COLLADA or VTK format. Would it be possible to add an import function for these scenes in ChimeraX, so we can create a static scene just the way we like it in Chimera1, and then render it with e.g. ambient occlusion etc in ChimeraX? Alternatively/additionally, would it be possible to add an export function for molecular surfaces to ChimeraX? One of the major improvements in ChimeraX (at least for my work) is that it has a robust and fast surface calculation function that works on large, multi chain structures. Would it be possible to export these surfaces (e.g as MRC format) so they could be imported into Chimera1? Cheers Oli

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Setting the bgColor transparent in ChimeraX
by bertrand beckert 03 Aug '18

03 Aug '18

Dear all, I have now been trying to use ChimeraX as a replacement for Chimera for making really nice images for publication. So far I have to say I really liked the rendering! definitely a really nice work! However I was really wondering how to get the background transparent... In Chimera we were able to set the background transparent as preference which is actually really useful... any idea how we can to do it in ChimeraX? Any help would be highly appreciated! Best Bertrand

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Transparency and Scaling factor in ChimeraX
by Christoph Bachmann 31 Jul '18

31 Jul '18

Dear ChimeraX team First of all, great piece of software. It's a lot more userfriendly than pyMol or VMD. But it is hard to find information, since most is still for the old Chimera. I'm struggeling to get transparency in saved pngs to work. I've tried it on a PC and a Mac with no luck. This is strange since both computers support transparency and I regularly work with that feature so it can't be a hardware problem. My main question is how to get absolute sizes of the molecules. I'm currently making an illustration with different molecules, from small to large and I want their size to be displayed as accurate as possible (so a carbon atom in one molecule is exactly as big as the one in another molecule). I'm sure there is an easy way but I haven't found anything so far. If I would load them all into ChimeraX their sizes are represented correctly, but that's just too much for the computer. So, thanks in advance for your help. Best wishes Christoph Bachmann University Basel - Switzerland

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How to not build bundles/use wheel?
by Yuri 25 Jul '18

25 Jul '18

I am trying to build on FreeBSD. It calls the module 'bundle_builder', which calls 'wheel'. How to only do a regular python build, and not call 'wheel'? Thanks, Yuri

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Volume isosurface transparency
by Zack Gainsforth 24 Jul '18

24 Jul '18

Hi, I’m fairly new to ChimeraX so forgive me if I’m a bit ignorant in this question. I have volumes acquired by tomographic reconstruction of STEM/EDS data (elemental composition in an electron microscope). I want to visualize several elements together as different colors representing phases. In some cases, the boundary is fairly obvious and can be represented with an isosurface. When I try to set the transparency of the isosurface so I can see the objects inside it, it simply turns darker color rather than transparent. As an example, here is a silicon isosurface obscuring the other volumes inside it: I’m setting the transparency using the colors dialog box: For comparison, if I make the isosurface invisible to show the objects inside: If instead I use the transparency command: volume #5 transparency 50 The isosurface turns black: My question is: am I doing this incorrectly? Thanks, Zack Gainsforth Space Sciences Laboratory, UC Berkeley 7 Gauss Way Berkeley, CA 94720 zackg(a)ssl.berkeley.edu

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Re: [chimerax-users] I suggest the addition of a "Automatic Styling (Smart Initial Display)" button
by Eric Pettersen 20 Jul '18

20 Jul '18

Hi Jean-Yves, The latest builds of ChimeraX have a “Presets” menu with an entry (“Original Look”) which allows you to easily return to the initial depiction of a model. —Eric Eric Pettersen UCSF Computer Graphics Lab > Greetings, > > > thank you for your quick reply about the "non-bug" request relating to the initial display and the explanation. After your reply I searched more intensely in the documentation and indeed found page help:user/autostyle.html with these details about the number of chains. > > > As I am preparing to demonstrate ChimeraX in the department (tutorial I find that some inherent aspect of the Automatic Styling (Smart Initial Display) is very quickly lost. e.g. simply by clicking on the "Show atoms" button in the Molecular display toolbar and then the "Hide atoms". > > > I found commands for selection at http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html <http://www.rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html> which are useful and one can reconstruct the initial display. > > > As I example I am using myoglobin (1mbo.) The molecule opens as a ribbon, heteroatoms as stick models, the iron ion as sphere, and AA close to the ligands as sticks as well. > > Simply pressing the "Show atoms" button will display all water molecules as small spheres. > > But now if I click "Hide atoms" only the ribbon is left. > > > Yesterday I tried to find a way to select heteroatoms in general and use the sel ~ sel selection inversion found on the pipermail<http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2017-December/000169.html <http://plato.cgl.ucsf.edu/pipermail/chimerax-users/2017-December/000169.html>> but that was not the best solution. > > > Today I could reconstruct the initial display with these commands if all I did was to toggle the "Show atoms" and "Hide atoms" buttons: > > > show ions > > show ligand > > select ligand:<3.8 & protein > > show selAtoms > > > For novices this is a bit complicated to understand. > > > Therefore I would like to suggest the addition of a "Automatic Styling (Smart Initial Display)" button, perhaps at the First position in the Molecular display toolbar. > > > I firmly believe that this would avoid lots of frustration for many new users! > > > P.S. One more thing: would it be possible to Copy from the built-in browser to Paste elsewhere as I am trying to do with the email address? > > > Sincerely, > > Jean-Yves Sgro

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Hardware for VR of volume data
by Tom Goddard 11 Jul '18

11 Jul '18

Hi Bernard, VR is not going to handle large volumes no matter what hardware you buy. To avoid causing nausea current VR headsets use 90 frames/second graphics updating. That is in two eyes, so the effective graphics frame rate needed is 180 frames/second. By comparison on a flat panel display it is routine to show a very large volume at 10 frames per second and this causes no problem. So VR requires about 20 times the rendering speed of visualization on a conventional display. So here are some ideas of what you can expect. Some recent 3d light microscopy I was looking at in VR is 4K by 2K by 31 z planes with 3 channels — and it rendered fast enough with VR on a GTX 1080 and also on a Quadro P6000. Comparing to your 2K cubed example my data was equivalent to about 2k x 2k x 186, or about 1/10th the size. I haven’t benchmarked volume rendering so I don’t actually know at what size graphics is too slow — I should test this. But I suspect this is close to the limit. For molecular structure display, 100,000 atoms with very coarsely triangulated spheres works in VR but is near the limit. For surface and triangle rendering the limit is about 2-5 million triangles depending on which high-end graphics card before frame drops start causing flicker. For molecules showing 2.4 million atoms of HIV capsid 3j3q is fine on a desktop display but is not going to work in VR. With that in mind I would recommend a GTX 1080 Ti graphics card with a high-end CPU, maybe 64 Gbytes of memory, definitely get a high-end SSD drive or two as the data transfer rates of about 3 Gbytes/second are very handy for large data compared to the 100 Mbytes/second of spinning drives — the whole system would be about $4-5k. You could spend more but you won’t get any better performance. The main VR performance bottleneck is going to be in the software if you use ChimeraX. Unfortunately it does color blending and mapping data values to colors and cropping on the CPU instead of the GPU which is painfully slow, tens of seconds to adjust brightness on the above-mentioned 3-channel light microscopy. I expect to put the blending and color lookup on the GPU in ChimeraX over the next 12 months. Tom > On Jul 10, 2018, at 12:48 PM, Heymann, Bernard (NIH/NIAMS) [E] wrote: > > Hi > > I'm interested in acquiring a PC with capabilities to use ChimeraX for 3D VR visualization of large volumes (2k cube). What is the best configuration (CPU, GPU, VR hardware) for around a $5-10k budget? > > Bernard > > > > > > _______________________________________________ > Chimera-users mailing list: Chimera-users(a)cgl.ucsf.edu > Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-users >

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