VMD-L Mailing List

From: dwang_at_cs.kent.edu
Date: Thu Jun 22 2006 - 20:36:59 CDT

Hi,

Currently I am working on a project involve superimposing two sets of
atoms from two proteins. I just wonder when we do the "measure fit", does
the order of the atoms within the same set matters? I noticed that when I
use the "list" option, the atoms are ordered in the increasing order. So
the correspondence between two lists seems lost. I suppose the algorithm
will treat all the atoms within one set equally, and try to minimize the
RMSD between the two atom sets.

thanks a lot

Dong Wang