[chimera-dev] question: development of a new icosahedral tool to include new lattices relevant for viruses

[Antoni Luque Santolaria]

Thanks, Tom.

1) The user interface will not be essential for the research that we'll be
carrying out in the short term, but it's something that I think it would be
beneficial in the longer run. Whenever you have a chance to port the
interface from Chimera to Chimera X let us know, and we'll adapt it for the
extended hkcage. In the meantime, we'll focus on extending the hkcage tool
to work through the command line.

2) Coloring the proteins in relation to hkcage as in the example that you
shared would be ideal. In fact, for herpes, the trihexagonal lattice would
show trimers that are missing in the color scheme of the image that you
shared. Our initial goal is to focus on viruses deposited in viperdb
because they have associated pdb files, but we would also like to include
some cryo-em capsids in the analysis because there are many more capsid
architectures that must to be reanalyzed. We'll follow the protocol that is
described in the link that you shared with us.

Best,
Toni

On Thu, Jun 25, 2020 at 9:32 AM Tom Goddard <goddard at sonic.net> wrote:

> 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
>
>   Chimera icosahedron surface docs
>
>
> https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/icosahedron/icosahedron.html
>
>     Tom
>
>
> On Jun 25, 2020, at 9:02 AM, Antoni Luque Santolaria <aluque at 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/IcosahedralCage/cages.py?rev=26214 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 at 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.py
>>
>>
>> https://plato.cgl.ucsf.edu/trac/chimera/browser/trunk/libs/IcosahedralCage/cages.py
>>
>>   Tom
>>
>>
>> On Jun 24, 2020, at 8:49 AM, Antoni Luque Santolaria <aluque at 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/) is part of the Viral Information
>> Institute at San Diego State University (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). 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
>> Assistant Professor
>> Department of Mathematics and Statistics
>> Viral Information Institute
>> San Diego State University
>>
>> Office: GMCS 514
>> Phone: 619 594 7244
>> email: aluque at sdsu.edu
>> _______________________________________________
>> Chimera-dev mailing list
>> Chimera-dev at cgl.ucsf.edu
>> https://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev
>>
>>
>>
>
> --
> Antoni Luque, PhD
> 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 at sdsu.edu
>
>
>

-- 
Antoni Luque, PhD
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 at sdsu.edu
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