[PyMOL] Problems with superposing small molecules and transformation

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

[PyMOL] Moving CGOs and getting matrix

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.

Re: [PyMOL] Problems with superposing small molecules and transformation

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