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.
Warren L. DeLano, Ph.D.
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 fax: (650)-266-3501
> -----Original Message-----
> From: Addis [mailto:addis@...]
> Sent: Thursday, December 13, 2001 10:13 AM
> To: pymol-users@...
> Subject: [PyMOL] add hydrogens
> 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
> 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
> PyMOL-users mailing list
From: Warren L. DeLano <warren@su...> - 2001-12-15 18:41:03
On Sat, 15 Dec 2001, Manfred W. Baumstark wrote:
> I would like to display an electron density as a surface instead of a mesh.
> Is this somehow possible with PyMOL?
> Thanks in advance for any help
This is planned but not yet possible.