On 2/2/06, S. Frank Yan <SYan@gnf.org> wrote:
I was wondering if PyMOL (with some plugin) has the capability to
visualize a series of small molecules that are associated with a protein
in a seamless way, e.g. poses from a docking exercise. Right now, what
we can do is to combine all the structures into a single file and open
with PyMOL. It would be a great tool to further advance PyMOL as a
I am not sure if I followed your question. But from what I understand, .sdf file is the perfect answer. Save the docked poses as .sdf file. Load the .sdf file along with the receptor structure. Then you can cycle through the small molecules in the .sdf file. What is more, even there is a wizard called filter, here you can save the good poses, reject the ugly ones and defer some if you arem't sure. I feel this is quite seamless.
Only hitch (and that is not the right word) is that if you want to effect a bond rotation or something on a pose, you can't do it since this is a multi-state object. Hope this helps. Do let me know if you have problem with this.