Hi German -
I’m not sure I follow exactly what you’re asking, but `align` does its
superimposition based on sequence alignment, which isn’t really meaningful for
small molecule ligands. I would suggest using `fit`, `super`, or `cealign`
instead, which all use just the coordinates, although it’
Apparently, one can go into edit mode, and select a CGO and move and translate
it. That's great, but I can't recover those transformations in a matrix, as I
can with molecular objects (cmd.get_object_matrix). Any suggestions?
_
Mark A. Saper, Ph.D.
Hi all,
I have two sets of ligands, the first are the crystal structures, the second
one are the same compounds, but aligned by a flexible ligand alignment, where
I used one of the crystal structures as a template. Unfortunately the
coordinates of the templates changed during the alignment.
Now I
