Eric, I'm glad to see you like the idea. It's a rather interesting
mechanism of adding H atoms, as you have noticed. It is correct that it
works only if the structure has no H atoms. The idea being that if a
structure has H atoms, then we shouldn't mess with it EVEN if
pdbAddHydrogens is set. As you point out, there are convenient ways around
that -- removing H atoms during the load with load FILTER "!_H" is a great
solution to that. The way to do this allowing H on water, if you really
think that is meaningful (convince me!) is to load the file first with no H
atoms but with set pdbAddHydrogens TRUE, then do
set pdbAddHydrogens TRUE
load =1lcd 1 filter "!_H"
delete HOH
set appendnew FALSE
load append "" 1 FILTER "[HOH]"
Notice that I'm just loading one model. For all three it looks like there
is a bug. I can't get it to work myself.
On Sun, Jun 23, 2013 at 5:32 PM, Eric Martz <[email protected]>wrote:
> I am very pleased with pdbAddHydrogens and the resulting double bonds
> on HETATM as well as ATOM. Wow! I would like to make this the default
> load for all PDB files in FirstGlance in Jmol.
>
> I find that Jmol does not add hydrogens if the model already contains
> hydrogen. For example
>
> set pdbAddHydrogens true
> load =1lfa
>
> does NOT add the missing hydrogens and the double bonds are NOT
> installed. (1lfa has hydrogens only on oxygens and nitrogens.)
>
> So I found that this works:
>
> set pdbAddHydrogens true
> load =1lfa filter "!_H"
>
> Now it appears that all the hydrogens are added and double bonds are
> installed.
>
> However, this mode does not add hydrogen to water, quite understandably.
>
> Some PDB files have hydrogen on water, e.g. 1lcd. Even if all the
> hydrogen in present in the PDB file, I want the double bonds to be
> installed. So here is my question:
>
> Can I load, filtering out all hydrogen that is NOT on water? I've
> tried what I can think of without success.
>
> Alternatively, perhaps we need a setting that will make
> pdbAddHydrogens work even when there are hydrogens in the data file
> (leaving any hydrogen on water untouched).
>
> Thanks, Eric
>
>
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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