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marrink-lab / vermouth-martinize

Describe and apply transformation on molecular structures and topologies
Apache License 2.0
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Visualizing Go bonds #609

Open Lp0lp opened 2 weeks ago

Lp0lp commented 2 weeks ago

Heyo! On the previous implementation of GoMartini, there was a way to obtain a non-production .itp file that contained the Go bonds as harmonic bonds that could be used for visualization. This functionality was lost when we ported it to Martinize. Would be cool to somehow bring it back, as it is a useful tool both for users and eventually for the MAD database.

Have a couple of ideas of how this could be brought back: 1) Have the Go bonds as harmonic bonds within the protein .itp within a -ifdefstatement (?) 2) Automatically write them in the .pdb file as connect entries (could run into issues if too many connects..)

Both of these could be turned off/on with a flag via martinize cli if we don't want them to be default.

What do you guys think?

csbrasnett commented 2 weeks ago

Hey Luis, I already implemented this in a small package I made! https://github.com/csbrasnett/martini_vis

csbrasnett commented 2 weeks ago

fwiw as well, this was also what I was thinking in #596 which could probably be happily extended to Go bonds once the general approach is dealt with

Lp0lp commented 2 weeks ago

Hey Chris! Good stuff, I will have a look! Thank you

Chris Brasnett @.***> escreveu (quarta, 28/08/2024 à(s) 09:53):

Hey Luis, I already implemented this in a small package I made! https://github.com/csbrasnett/martini_vis

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