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GLYCAM-Web / website

A bare-bones repo to contain public website stuff and issues related to the GLYCAM Web Django apps.
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MolStar and derivative groups #181

Open gitoliver opened 4 months ago

gitoliver commented 4 months ago

Is your feature request related to a problem? Please describe. It looks like the sulfates aren't bonded when you build this: DGalpNAc[4S,6S]b1-OME Default structure is fine, but the energy minimized one likely contains TER cards which MolStar is reasoning about. Perhaps we can force MolStar to draw bonds, or we load in a different file e.g. min-gas.mol2. Or this is something to fix at the MD_Utils (tleap doesn't add the TER cards) or gmml level (gmml doesn't add the TER cards)

gitoliver commented 4 months ago

If I upload min-gas.pdb to the molstar viewer https://molstar.org/viewer/ I see the same problem of the sulfates not being connected. If I upload the min-gas.mol2 file instead, it displays correctly. Maybe if we switch to showing that the problem is solved easily.