Opened 7 years ago

Closed 7 years ago

#1125 closed defect (fixed)

Functionality 'nucleotides' not working

Reported by: arosa@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Depiction Version:
Keywords: Cc: Elaine Meng, Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

Hi everybody,

I’m not able to represent the side chains of an RNA  molecule as a ladder with the command ’nucleotides’. I’ve tried it in ChimeraX 0.6 and ChimeraX 0.7 daily and it is simply not represented.

In the image below I’m testing the command on a 5S ribosomal RNA and I got the error of an empty Array. Sometimes I don’t get any error, the command seems to be recognized (in the log) but nothing changes on the molecule itself.

I also tried to show all atoms, hide atoms, hide ribbon, delete hbonds, look for hbonds again, specify the model (#1) only, specificy the hydrogen bonds (#1.1) but nothing seems to work. Am I doing something wrong?

Thank you for your consideration.

André Rosa

[cid:image002.png@01D3ED19.13D3A880]

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Attachments (1)

CB1900E4FF5B4986A3EBB73562E9E096.png​ (141.1 KB ) - added by arosa@… 7 years ago.
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Change History (5)

by arosa@…, 7 years ago

Attachment: CB1900E4FF5B4986A3EBB73562E9E096.png​ added

Added by email2trac

comment:1 by pett, 7 years ago

Cc: Elaine Meng added
Component: Unassigned → Depiction
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned

comment:2 by Greg Couch, 7 years ago

Status: assigned → accepted

This was working a couple of weeks ago. Will look into it next.

comment:3 by Greg Couch, 7 years ago

Cc: Tom Goddard added

This might be because of a Drawing API change. With a minor fix for vertex_colors, there is no longer a traceback, but only the first shape (slab, rung, etc.) is shown.

comment:4 by Greg Couch, 7 years ago

Resolution: → fixed
Status: accepted → closed

Fixed. "New" Drawing.set_geometry() cleared vertex_colors, which the ShapeDrawing code did not expect. The fix will be in the next daily build.

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