Addis, Yes, I am aware of this issue and plan to address it in later versions. Hydrogen adding needs to become residue-aware.
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:war...@sunesis.com 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...@dsi.unifi.it] > Sent: Thursday, December 13, 2001 10:13 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] add hydrogens > > > I start to work in computational chemistry and I use as imput > file of my > algorithm a pdb standard format, I need all atoms for my calculation > (also hydrogens), but frequently the examples I found are without > hydrogens. I have used the command h_add and it works: it add > hydrogens, > but the names are diffrent from the standard pdb format. I explain in > pdb format the name of hydrogen depends on the position that > it has in > the aminoacyd structure ( for example 1HB is the first > hydrogen linked > to C-beta , but if I add hydrogens with h_add I obtain a sequence of > 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 > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
