RE: [PyMOL] 1pit.pdb

[DeLano, W. <wa...@su...>]

Jack,

What are all those extra "Q" atoms in the pdb file?  They look to me =
like compromise/placeholder coordinates for NMR-equivalent =
hydrogens...or something like that.

To get a reasonable picture, you can get rid of the extra bonds with=20

   unbond elem q*,all

or just nuke the "Q" atoms altogether

   remove q*

Cheers,
Warren

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.=20
Informatics Manager=20
Sunesis Pharmaceuticals, Inc.=20
341 Oyster Point Blvd.=20
S. San Francisco, CA 94080=20
(650)-266-3606 FAX:(650)-266-3501



> -----Original Message-----
> From: Jack Howarth [mailto:ho...@br...]
> Sent: Sunday, January 12, 2003 6:17 PM
> To: pym...@li...
> Subject: [PyMOL] 1pit.pdb
>=20
>=20
>     Under linux does anyone else see the following? If one
> loads in the 1pit.pdb from the MOLMOL data files, the
> resulting structure seems to have extra bonds drawn in the
> side chains. For example phe's seem to have all the opposing
> carbons in the rings interconnected through the center of
> the ring. Thanks in advance for any hints on what is causing
> that.
>                                      Jack
>=20
>=20
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>=20