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

Thu, 02 February 2023 20:37

nbehrnd
Messages: 224
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.

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[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

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