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ribokit / RiboDraw

Semiautomated layout of RNA tertiary structure diagrams
MIT License
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Limited RNA modifications available in rna_motif #51

Open joegeorgeson opened 2 years ago

joegeorgeson commented 2 years ago

Hi RiboDraw,

Really neat tool!

I was wondering if anyone has been able to use rna_motif with an expanded set of RNA modifications? It seems that the default library of Rosetta doesn't contain everything that exists in PDB. Any thoughts on how to address/circumvent this?

For example, 6SKF fails with the below errors;

core.chemical.GlobalResidueTypeSet: Loading (but possibly not actually using) '4AC' from the PDB components dictionary for residue type 'pdb_4AC'
core.chemical.GlobalResidueTypeSet: [ WARNING ] Could not find: 'LHH' in pdb components files! Skipping residue...

ERROR: Unrecognized residue: LHH
ERROR:: Exit from: src/core/io/pose_from_sfr/PoseFromSFRBuilder.cc line: 1449

[ ERROR ]: Caught exception:

File: src/core/io/pose_from_sfr/PoseFromSFRBuilder.cc:1449
[ ERROR ] UtilityExitException
ERROR: Unrecognized residue: LHH
everyday847 commented 2 years ago

Short of making some modifications to Rosetta, you likely will want to skip that residue manually -- possibly relabeling it to a canonical type and altering the label manually after you have exported an SVG.

The trouble, ultimately, is that the PDB expands its purview of chemically modified nucleic acids quite often, and there aren't any Rosetta developers devoted specifically to ensuring that that it keeps pace. Our github versions update much faster than our releases, so if you have git access to Rosetta I might be able to solve this problem for you in a matter of days, but if you're reliant on the "weekly" releases it might take a bit longer.

joegeorgeson commented 2 years ago

I'll ask some of my Rosetta-oriented colleagues if they can push some updates ...will update if anything happens. Thanks!