Re: [PyMOL] A suggestion

[Ramesh S. <sis...@gm...>]

On 2/2/06, S. Frank Yan <SY...@gn...> wrote:
>
> Hi,
>
> 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
> visualization tool.
>
>
Hi Frank,

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 wit=
h
this.

best wishes


Ramesh Sistla