Opened 8 years ago

Last modified 7 years ago

#1119 closed defect

Misleading pseudobond at RNA chain break in mmCIF 5an9 — at Version 3

Reported by: Tristan Croll Owned by: Greg Couch
Priority: major Milestone:
Component: Input/Output Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description (last modified by Greg Couch)

Opening 5an9, residues N2700 and N2925 (the 3' and 5' sides of a chain break) are messed up. The pseudobond across the break goes from the O3' atom of N2700 to O3' of N2925.

Change History (3)

comment:1 by Eric Pettersen, 8 years ago

Component: Core → Input/Output
Owner: changed from Eric Pettersen to Greg Couch
Summary: Erroneous bonding at RNA chain break in 5an9 → Erroneous bonding at RNA chain break in mmCIF 5an9

The problem description most closely matches the behavior of the mmCIF version of 5an9, though the current daily build does correctly bond N2925-26 (the pseudobond is nonetheless still wonky). The PDB version has different incorrect behavior, so I will open a separate ticket for that since Greg handles mmCIF and I do PDB.

--Eric

comment:2 by Greg Couch, 8 years ago

The mmCIF reader tries to generate a pseudobond connecting the linking atoms of N2700 and N2925. Unfortunately, N2925 is missing the P, so the pseudobond is connecting to the closest atom. A possible solution would be to use the residue template to find the closest existing atom to the P to connect the psuedobond to.

comment:3 by Greg Couch, 8 years ago

Description: modified (diff)
Summary: Erroneous bonding at RNA chain break in mmCIF 5an9 → Misleading pseudobond at RNA chain break in mmCIF 5an9
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