openmolecules.org Forum: Cheminformatics » Generate 2D atom coordinates gives overlapping atoms

Home » DataWarrior » Cheminformatics » Generate 2D atom coordinates gives overlapping atoms

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

Generate 2D atom coordinates gives overlapping atoms [message #1826]

Tue, 31 January 2023 12:01

mcmc
Messages: 23
Registered: April 2018

Junior Member

/forum/index.php?t=getfile&id=654&private=0

I have some bridged piperazines that get redrawn in a way that atoms are overlapping with the attached heterocycle upon generating 2D atom coords (which I do to superimpose the compounds in a set).
Hard to explain in words, but picture attached.
If these overlapping atoms could be avoided, that would be much appreciated.

Attachment: bridged ring funky.jpg
(Size: 12.29KB, Downloaded 987 times)

Report message to a moderator

[Message index]

		Generate 2D atom coordinates gives overlapping atoms By: mcmc on Tue, 31 January 2023 12:01
		Re: Generate 2D atom coordinates gives overlapping atoms By: nbehrnd on Thu, 02 February 2023 20:37
		Re: Generate 2D atom coordinates gives overlapping atoms By: mcmc on Fri, 03 February 2023 10:51
		Re: Generate 2D atom coordinates gives overlapping atoms By: nbehrnd on Fri, 03 February 2023 22:32
		Re: Generate 2D atom coordinates gives overlapping atoms By: mcmc on Fri, 10 February 2023 16:43
		Re: Generate 2D atom coordinates gives overlapping atoms By: nbehrnd on Fri, 10 February 2023 23:00

Previous Topic:	Optional automatic protonation feature of Nitrogen in DW using EL
Next Topic:	Link to oracle per row

Goto Forum:

-=] Back to Top [=-

[ Syndicate this forum (XML) ] [

] [

]

Current Time: Tue Jan 13 07:34:31 CET 2026

Total time taken to generate the page: 0.52966 seconds