Hi team (and support),
I have found that when I “get a pdb” file or use a .cif file with the latest
versions (3.1) and then add hydrogens, it behaves differently to previously
where the amines and acids are not ionised (should be ammonium/guanidinuim and
carboxylate).
But it does it with some
Hi all,
I have just noticed that when you add hydrogens to a protein file that is a
.mol2, hydrogens are added to carboxylates to make them the acid (unionised).
This does not occur for a pdb file (they are ionised).
Can this be fixed in a future version? I would have thought that the atom
typ
s. That will come in time.
Cheers,
Warren
> -Original Message-
> From: pymol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> S. Frank Yan
> Sent: Wednesday, April 07, 2004 12:10 PM
> To: pymol-users@lists.sourceforge.net
&
Hi,
I was wondering if there is a way to add hydrogens to
a selected atom based on different hybridization,
e.g., sp2, sp3, etc., in which way different number of
hydrogens will be added with the corresponding
geometry.
Thanks,
Frank
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> -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
