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Export Superimposed structures [message #1593] Thu, 14 April 2022 05:11 Go to next message
sbembenek18 is currently offline  sbembenek18
Messages: 63
Registered: April 2019
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I have aligned my molecules to a 3D reference using 'Superimpose Conformers'. Can I now write an SDF file with these new aligned (updated) coords for each molecule rather than the original 3D coords?

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Re: Export Superimposed structures [message #1609 is a reply to message #1593] Sun, 15 May 2022 17:08 Go to previous message
thomas is currently offline  thomas
Messages: 747
Registered: June 2014
Senior Member
Yes. Admittedly, it is not really obvious. The Superimpose method creates a new (hidden) column 'Best Match'. It is hidden, because in most cases it contains just the same structure from the 'Structure' column. The new aligned 3D-coordinates are stored as another hidden column assigned to 'Best match'. Thus, use 'File->Save Special->SD File'. In the dialog choose 'Best match' as structure column and 'Superposition' as coordinates. Then you may also choose 'Include Reference Molecule' to also include the superposition target molecule oin the SD-file.

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