AW: vmd-l: matching part of two models

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Mon Aug 26 2013 - 04:58:04 CDT

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Hi,

what’s about RMSD Alignment? You could do it by hand or write a script for it. Just load both molecules to separate mol ids. Then align the parts you want. Save the coordinates of both molecules to pdb. Now replace the parts in the pdbs.

Norman Geist.

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von Francesco Pietra
Gesendet: Montag, 26. August 2013 08:48
An: vmd-l_at_ks.uiuc.edu
Betreff: vmd-l: matching part of two models

Hello;

I am looking for a VMD plugin/script to match (superimpose) a portion (such as a few alpha-helix turns) of a large polypeptide model 1 with a small polypeptide model 2. All that in order to replace the model-2 part in model 1.

This means that model 2 was modeled separately while maintaining by rmsd-colvars the conformation of the helical portion that I would like to superimpose.

Thanks

francesco pietra

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