Opened 3 weeks ago

Closed 3 weeks ago

#20483 closed defect (fixed)

The slab position for PSU residues is wrong

Reported by: Daniel Larsson <daniel.larsson@…> Owned by: Greg Couch
Priority: major Milestone:
Component: Depiction Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description

A follow-up to the visualization of modified nucleotides as “slab”. The base of pseudouridine has the slab pointing in the wrong direction (probably due to the isomerization of the pyrimidine ring). This makes visualization of base pairs to PSU look wrong since the bases do not line up correctly (see attached image with PSU in purple in wrong position).


Attachments (1)

image261.png​ (14.4 KB ) - added by Greg Couch 3 weeks ago.
Example of misaligned slab

Download all attachments as: .zip

Change History (4)

by Greg Couch, 3 weeks ago

Attachment: image261.png​ added

Example of misaligned slab

comment:1 by Greg Couch, 3 weeks ago

Status: assigned → accepted

I can replicate with pdb:1bzt.

I suspect that this problem can occur with other modified nucleotides. Can this be detected by comparing the chirality?

comment:2 by Eric Pettersen, 3 weeks ago

Component: Unassigned → Depiction

comment:3 by Greg Couch, 3 weeks ago

Resolution: → fixed
Status: accepted → closed

It turns out that PSU was already a special case in the nucleotides code, so fixed that rather than do a general solution for modified nucleotides with flipped pyrimidines. The fix will be in the imminent ChimeraX 1.12 and the next daily build.

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