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schrodinger / pymol-open-source

Open-source foundation of the user-sponsored PyMOL molecular visualization system.
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PEPTIDE NUCLEIC ACID (1PNN) broken cartoon #187

Open giagitom opened 3 years ago

giagitom commented 3 years ago

Hi, This non-standard structure has a broken secondary structure when loaded on PyMol. Molstar is able to generate a secondary structure like this one

image

TstewDev commented 3 years ago

Hi @giagitom, can you provide the file for the structure? Or the PDB ID?

Scratch that, I see that it is in the title of the issue! I'll take a look at it and get back to you.

giagitom commented 3 years ago

Hi @TstewDev
Sorry, It was in the title: 1PNN

giagitom commented 3 years ago

Hi @TstewDev , Any news about this?

TstewDev commented 3 years ago

Hi @giagitom, Sorry for not getting back to you right away on this! I looked into it when you first posted but could not come up with a quick fix. This structure is very unique both in terms of proximity of the chains but also because chains A and C loop back on themselves. I still need to figure out which of these is causing the issue and see if there is something that can be tweaked to fix it. I'll create a ticket for this and hopefully have a deeper look at it soon. I'll update you here if I make any progress. Thanks, Thomas Stewart

giagitom commented 3 years ago

Hi @TstewDev , thanks for letting me know. I found out in the Protein Data Bank other structures like this presenting the same issue, maybe this could be helpful to you PDB IDs: 5EMG 1XJ9 176D 5EME 1PUP

giagitom commented 3 years ago

Could it be something related to backbone atoms that are non standard and PyMol is unable to detect them?

TstewDev commented 3 years ago

Actually yeah this seems more likely, especially with the other examples you gave (looking at 1PUP right now). So that means this will likely not be a quick fix but may still be worth addressing. Thanks for your help in identifying the issue! I'm going to leave this issue open until we determine what direction we want to go in with non-native nucleotides.