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

Re: Generate 2D atom coordinates gives overlapping atoms [message #1831 is a reply to message #1826]

Thu, 02 February 2023 20:37

nbehrnd
Messages: 211
Registered: June 2019

Senior Member

Hello mcmc,

your question does not describe how the piperazines on the left are generated in first place. Is it a SMILES string, a .sdf file you import? Do you draw them with DW's sketcher? Opting for the latter, starting to draw the molecule from the right, the furopyrazole, to which I added piperazine, and lastly, the bridge to piperazine, I did not observe the overlap you describe.

Regards,

Norwid

DW for Linux/MacOS version 5.5 with updates published by 2023-01-18 in Linux Debian 12/bookworm.

Attachment: piperazine.png
(Size: 14.58KB, Downloaded 99 times)
Attachment: piperazine.dwar
(Size: 1.34KB, Downloaded 104 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: Fri May 17 12:03:43 CEST 2024

Total time taken to generate the page: 0.04590 seconds