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

Fri Jun 26 10:30:49 PDT 2020

Great, thanks for the info!

On Fri, Jun 26, 2020 at 9:38 AM Tom Goddard <goddard at sonic.net> wrote:

> Hi Toni,
>
>   Ok, plan sounds good.
>
>   Regarding the coloring, it is usually easy to do when you have an atomic
> model of the asymmetric unit, you just color each chain as needed.  That
> requires no additional capabilities in Chimera / ChimeraX.  To generate the
> icosahedral layout from the asymmetric unit (1/60 of capsid) use the sym
> command.  To color a cryoEM map the easiest approach is to use the "color
> zone" capability to color the map according to the atomic model.  It is
> only when you don't have an atomic model for the map that the coloring gets
> tricky.  That is a rare case since usually the first thing that is done
> with these maps is to fit an atomic model.  That herpes simplex virus image
> I sent was one of those rare cases, the researchers were studying the virus
> portal and did not include atomic models in their publication.  So
> developing easier coloring may not be needed.
>
> Tom
>
>
> On Jun 25, 2020, at 6:06 PM, Antoni Luque Santolaria <aluque at sdsu.edu>
> wrote:
>
> 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
>> <emd1307.jpg>
>>   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
>
>
>

-- 
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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