openmolecules.org

 
Home » DataWarrior » Functionality » Export Superimposed structures
Export Superimposed structures [message #1593] Thu, 14 April 2022 05:11 Go to next message
sbembenek18 is currently offline  sbembenek18
Messages: 62
Registered: April 2019
Member
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?

Report message to a moderator

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: 731
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.

/forum/index.php?t=getfile&id=550&private=0
  • Attachment: temp.png
    (Size: 41.91KB, Downloaded 376 times)

Report message to a moderator

Previous Topic: defining molecule clusters after similarity analysis
Next Topic: macro buildEvolutionaryLibrary from a mac terminal
Goto Forum:
  

[ Syndicate this forum (XML) ] [ RSS ] [ PDF ]

Current Time: Mon Jun 09 08:17:00 CEST 2025

Total time taken to generate the page: 0.06929 seconds
openmolecules.org