openmolecules.org Forum: Bug Reports » Generating 2D Coords does not work with 3D structures

Home » DataWarrior » Bug Reports » Generating 2D Coords does not work with 3D structures (Generating 2D Coordinates)

Show: Today's Messages :: Polls :: Message Navigator

Generating 2D Coords does not work with 3D structures [message #1244]

Mon, 08 March 2021 11:56

richards99
Messages: 42
Registered: May 2020
Location: UK

Member

It seems that when I what to regenerate 2D coordinates for structures from Chemistry/Generate 2D Coordinates, and provide a Substructure to align too, this does not seem to work if the structures already have 3D coordinates.

Workaround currently, is I generated SMILES of these structures, do Name to Structure, and then generate 2D coordinates on these.

Simon.

Report message to a moderator

Re: Generating 2D Coords does not work with 3D structures [message #1246 is a reply to message #1244]

Tue, 09 March 2021 17:20

thomas
Messages: 747
Registered: June 2014

Senior Member

Thank you. There was an issue of not applying a template's 2d-atom-coordinates, if the template consisted of the same atoms that were later automatically discovered as part of a fragment coordinate rule within the coordinate inventor (e.g. a ring or a connecting chain. This is now fixed in the current development version. If you still have issues, please send me a reproducible example. Whether 3D-coordinates exist should not make a difference.

Thomas

Report message to a moderator

Previous Topic:	Undo function
Next Topic:	Merge Structure Error

Goto Forum:

-=] Back to Top [=-

[ Syndicate this forum (XML) ] [

] [

]

Current Time: Thu Jul 09 18:32:20 CEST 2026

Total time taken to generate the page: 0.00479 seconds