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ncbi / icn3d

web-based protein structure viewer and analysis tool interactively or in batch mode
https://www.ncbi.nlm.nih.gov/Structure/icn3d
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Ideas for improving the cartoon #87

Closed ctrlcctrlv closed 1 year ago

ctrlcctrlv commented 1 year ago

When chain label names* overlap in the 2D cartoon view, that looks ugly on SVG output:

image

It's not so hard to manually correct though:

_cartoon

My example image is setrusumab which I imported the PDB of from @oxpig's ABlooper. Sorry I don't have the experience to judge if that is actually a good representation of setrusumab. It looks like a SOST antibody to me but lol I have no degree.

If these could be improved it'd help illustrate Wikipedia a lot I imagine. What is the licensing, by the way, of screenshots of ICN3D?

ctrlcctrlv commented 1 year ago

(Correction : @brennanaba wrote ABlooper.)

jiywang3 commented 1 year ago

Thanks for your suggestions. It's hard to arrange the labels automatically in iCn3D. So some manual adjustment might be required.

Anything in iCn3D has no license restriction except the commercial use of DelPhi electrostatic potential as stated at https://github.com/ncbi/icn3d/blob/master/LICENSE.md.

The output should be stable. The 2D cartoon of secondary structures in your example depend on the orientation of the 3D structure since the 3D objects are projected to a plane.

jiywang3 commented 1 year ago

You can change the size of the labels, or move the helices/sheets around in the SVG view. The labels simply label the helices (H#) and sheets (S#) with the postfix of residue numbers. For example, "S100" means it's a beta sheet starting at the residue number 100.

youkha commented 1 year ago

Fredrick,

iCn3D is open source, meaning it is available to all for further development, yet we hope that programmers that develop new or better features can share them with the community. We would integrate any improvement (and support it) if they are valuable. So in other words we welcome and hope for suggestions that have been reduced to practice as a prototype. We have hackathons during the year where that is common practice. What you see was in part prototyped during a hackathon

On 2D cartoons, we absolutely need improvements, yet a general 2D is not easy to implement. If you are interested in pushing further, we could discuss these improvements.

Interestingly, you picked an antibody which is made of Immunoglobin (Ig) domains. The projection is NOT a good representation of Ig domains and as I said we do not have a good general projective method BUT on important domains, especially Ig domains, we have developed 2D Ig templates that we hope we can make available at some point in the software. Some efforts were done in the last 2 ISMB hackathons:

I must say that these maps are extremely useful. We are developing templates for other very important domains right now. Note that Ig domains are components of 2% of the human genome, the single most abundant domain, especially in the immune system and the nervous system. We also thought that for education, including wikipedia, 2D cartoons would be very useful. We need cartoons in 2D as we need them in 3D. All that is part of the original roadmap (Twelve Elements ...) and is one of the elements still not achieved ...

We will develop a new roadmap shortly, and hopefully this Element may become central. If you have followed AI developments, you may have seen that we went from 200,000 3D structures (PDB) available to 200,000,000 (ALPHAFOLD/UNIPROT) recently and hence high quality 2D cartoons of these would be a tremendous step forward for the community, especially the young generation.

Best, Philippe

On Sat, Oct 8, 2022 at 9:33 AM Jiyao Wang @.***> wrote:

You can change the size of the labels, or move the helices/sheets around. The labels simply label the helices (H#) and sheets (S#) with the postfix of residue numbers. For example, "S100" means it's a beta sheet starting at the residue number 100.

— Reply to this email directly, view it on GitHub https://github.com/ncbi/icn3d/issues/87#issuecomment-1272321223, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD35NIK3Q3INXGZLAOTEFW3WCFZZDANCNFSM6AAAAAARACII7U . You are receiving this because you are subscribed to this thread.Message ID: @.***>

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ctrlcctrlv commented 1 year ago

Can I ask why you don't think it's a good representation? I made some art from it :joy: setrusumab

Thanks for all the advice by the way. I'm glad federal grants support software like this.

youkha commented 1 year ago

Hi, The 3D cartoon representation you use here is good, so you are OK on your "art work", the 2D you originally mentioned is the one I commented on. While our aims are beyond art, we like the art-science connection. I am glad you find an application of our software. You may want to play with backgr4ound colors and maybe with VR?

On Sun, Oct 9, 2022 at 8:05 PM Fredrick Brennan @.***> wrote:

Can I ask why you don't think it's a good representation? I made some art from it 😂 [image: setrusumab] https://user-images.githubusercontent.com/838783/194785607-638e2418-411a-4f2b-a340-d43168055b99.jpeg

Thanks for all the advice by the way. I'm glad federal grants support software like this.

— Reply to this email directly, view it on GitHub https://github.com/ncbi/icn3d/issues/87#issuecomment-1272659417, or unsubscribe https://github.com/notifications/unsubscribe-auth/AD35NIOVICAQD7ZYVM6A64DWCNMV5ANCNFSM6AAAAAARACII7U . You are receiving this because you commented.Message ID: @.***>

-- -- Philippe Youkharibache, Ph.D. US +1 415 448 6509 FR +33 666 00 4775