RE: [PyMOL] add hydrogens

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

Addis,

  Yes, I am aware of this issue and plan to address it in later
versions.  Hydrogen adding needs to become residue-aware. =20

Note that when you are building amino acids, they do start out with
qausi-correct hydrogen names.  There is still some ambituity as to which
convention is followed for 4-letter names 2HH1 vs. HH12.  Unfortunately,
certain packages make assumptions about this, so PyMOL should probably
support both, as well as on-the-fly interconversion.

Cheers,
Warren

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



> -----Original Message-----
> From: Addis [mailto:ad...@ds...]
> Sent: Thursday, December 13, 2001 10:13 AM
> To: pym...@li...
> Subject: [PyMOL] add hydrogens
>=20
>=20
> I start to work in computational chemistry and I use as imput=20
> file of my=20
> algorithm a pdb standard format, I need all atoms for my calculation=20
> (also hydrogens), but frequently the examples I found are without=20
> hydrogens. I have used the command h_add and it works: it add=20
> hydrogens,=20
> but the names are diffrent from the standard pdb format. I explain in=20
> pdb format the name of hydrogen depends on the position that=20
> it has in=20
> the aminoacyd structure ( for example 1HB is the first=20
> hydrogen linked=20
> to C-beta  , but if I add hydrogens with h_add I obtain a sequence of=20
> hydrogens labeled as H01,H02,...
> Is it possible to obtain labels in standard pdb format?
> Thank you very much,
> 	Bernardetta Addis
>=20
>=20
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>=20