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September 2020

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Re: [chimera-dev] question: development of a new icosahedral tool to include new lattices relevant for viruses
by Tom Goddard 31 Oct '20

31 Oct '20

Hi Toni, That all sounds good. Yes the link you found is our svn source code for cages.py. Sorry, I accidentally gave you the https link which takes a password and allows checking in changes to the code. The additional options to the hkcage command should be no trouble. It will be pretty obvious how to add them in ChimeraX. In Chimera the code may be harder to fathom, but Colin can ask when stuck on anything. The user interface panel is the most work of what you describe. The current Icosahedron Surface tool in Chimera does not offer the hkcage options, just a plain icosahedron. The hkcage command was developed after that user interface and never got incorporated in. For that user interface window Chimera and ChimeraX will be completely different because Chimera uses the Tk window toolkit while ChimeraX uses the Qt window toolkit. I suggest giving priority to the ChimeraX version of that tool, although the plain icosahedron user interface has not been ported to ChimeraX yet. Possibly I can port it to ChimeraX making all the Tk to Qt changes as a starting point for Colin. Probably I would not have time to do that until mid-July. The Chimera icosahedron surface tool has a subdivision parameter that divides the facets into smaller triangles. The current hkcage does not support that and some extra code would be needed to compute such subdivisions of the hexagons, pentagons, .... It may also be interesting to think about how to color electron microscopy maps to show the virus capsomere arrangement, for example as in this image https://www.cgl.ucsf.edu/chimera/ImageGallery/entries/herpes/herpes.html ChimeraX hkcage docs https://www.cgl.ucsf.edu/chimerax/docs/user/commands/hkcage.html Chimera hkcage docs https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/hkcage.html> Chimera icosahedron surface docs https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/icosahedron/icosa… Tom > On Jun 25, 2020, at 9:02 AM, Antoni Luque Santolaria <aluque(a)sdsu.edu> wrote: > > Hi Tom, > > 1. Thank you for the quick response and clear instructions. I wasn't aware of ChimeraX. I just installed it, and it looks fantastic. > > 2. Colin Brown (in CC) is a master student in the lab who will be leading the efforts to develop the new icosahedral tool over the summer. He will contact you if we have any questions during the development process. > > 3. I wasn't able to access the second link that you shared with us. It requires a username and password. But I found the cages.py in this other link: http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/contrib/IcosahedralCag… <http://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/contrib/IcosahedralCag…> Is it the same code? > > 4. The extension that we have in mind would include an option, as you suggest, to identify the lattice (h, t, s, r,...), an option to indicate if the construction uses the regular (hexagons, pentagons) or dual (single tile) blocks, and a third parameter for lattices that have a degree of freedom (see for example Figure 5a in Twarock and Luque, 2019). We would also like to add a panel to control the options manually like in the icosahedron tool. The goal of this gui panel would be to facilitate users to modify the radius, sphere factor, and other options on the fly to obtain a good visual agreement with the viral structure or macromolecular complex of study. Let us know if this would be reasonable. > > Best, > Toni > > On Wed, Jun 24, 2020 at 2:30 PM Tom Goddard <goddard(a)sonic.net <mailto:goddard@sonic.net>> wrote: > Hi Toni, > > Neat! I wrote the hkcage code and I think adding your 3 additional series t,s,r to that command would be the way for researchers to get the most use out of it. It could simply be adding one more option to that command that specifies the series. The code that would be needed is Python that computes the vertex coordinates, a triangulation (a list of 3-tuples of vertex indices), and an edge mask that says which of the triangle edges should be hidden (one integer per triangle with 3-bits 0x1, 0x2, 0x4 indicating if the triangle edge should be shown). I could incorporate your code into the Chimera and ChimeraX distributions and we would credit you cite your paper in the documentation. I think it would be quite easy for you to simply modify the cage.py code in your Chimera or ChimeraX distribution, do all the testing, write a bit of documentation describing the new option -- send that to me and I will get it into the daily builds and subsequent releases. > > ChimeraX is the successor of Chimera and ChimeraX 1.0 was just released. Most researchers are still using Chimera instead of ChimeraX but we expect that to transition over the next few years, so I would suggest making your addition to the ChimeraX code. But you can make the additions to ChimeraX or Chimera and I can move it to the other if you like, the hkcage code for the two is nearly identical. ChimeraX uses Python 3 while Chimera uses Python 2. > > https://www.rbvi.ucsf.edu/trac/ChimeraX/browser/src/bundles/hkcage/src/cage… <https://www.rbvi.ucsf.edu/trac/ChimeraX/browser/src/bundles/hkcage/src/cage…> > > https://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/IcosahedralCage/… <https://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/IcosahedralCage/…> > > Tom > > >> On Jun 24, 2020, at 8:49 AM, Antoni Luque Santolaria <aluque(a)sdsu.edu <mailto:aluque@sdsu.edu>> wrote: >> >> Dear Chimera development team, >> >> My lab is interested in developing (or extending) a new version of the hkcage command in cages.py to include the different icosahedral lattices that have been recently discovered and have important implications for viral structures (see Twarock and Luque, Nature Communications, 2019). We would like to receive advice on what would be the best approach to help integrate the tool to be used and shared with the Chimera community. Would it be better to extend hkcage? Generate a new function? Integrate the function in cages.py? Generate a different python script? >> >> My lab (https://www.luquelab.com/ <https://www.luquelab.com/>) is part of the Viral Information Institute at San Diego State University (https://viralization.org/ <https://viralization.org/>) and recently discovered, in collaboration with Prof. Reidun Twarock (The University of York), a new set of icosahedral lattices that describe previously uncharacterized viral capsid structures (https://www.nature.com/articles/s41467-019-12367-3 <https://www.nature.com/articles/s41467-019-12367-3>). My lab's goal is to develop a tool in Chimera that reflects these new geometries and helps us analyze viral capsids and other complexes with icosahedral symmetry. We would also like to facilitate the scientific community to use this tool in Chimera. This project will be developed as part of an NSF award. >> >> Please let us know the best way to proceed. >> >> Thanks, >> Toni >> >> >> -- >> Antoni Luque, PhD >> http://luquelab.com <http://luquelab.com/> >> Assistant Professor >> Department of Mathematics and Statistics >> Viral Information Institute >> San Diego State University >> >> Office: GMCS 514 >> Phone: 619 594 7244 >> email: aluque(a)sdsu.edu <mailto:aluque@sdsu.edu>_______________________________________________ >> Chimera-dev mailing list >> Chimera-dev(a)cgl.ucsf.edu <mailto:Chimera-dev@cgl.ucsf.edu> >> https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev> > > > > -- > Antoni Luque, PhD > http://luquelab.com <http://luquelab.com/> > Assistant Professor > Department of Mathematics and Statistics > Viral Information Institute > San Diego State University > > Office: GMCS 514 > Phone: 619 594 7244 > email: aluque(a)sdsu.edu <mailto:aluque@sdsu.edu>

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Detecting Differences in Hydrogen Placement in PDB Files
by Alexander Novokhodko 25 Sep '20

25 Sep '20

Dear Chimera User List, Could you please help me figure out how to detect differences in hydrogen placement between two Chimera files? I have two structures of the same protein with hydrogens placed by different programs, and I have differences in hydrogen bonding that I'm trying to explain. Thus, I would like to know where the hydrogens were placed and in particular, where they were placed differently. Please help! Thank you, Sincerely, Alexander Novokhodko

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