From: DeLano, W. <wa...@su...> - 2001-12-13 21:42:42
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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 > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users >=20 |
From: Manfred W. B. <ma...@uk...> - 2001-12-15 17:50:28
Attachments:
maba.vcf
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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 Manfred |
From: Warren L. D. <wa...@su...> - 2001-12-15 18:41:03
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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. Cheers, Warren |