Just a bad test script on my part. Here you go:
set pdbaddhydrogens
load =1lcd 1 filter "!_H"
set appendnew false
delete HOH & 1.1
load append "" 1 filter "[HOH]"
set appendnew true
load append "" 2 filter "!_H"
set appendnew false
delete HOH & 2.1
load append "" 2 filter "[HOH]"
set appendnew true
load append "" 3 filter "!_H"
set appendnew false
delete HOH & 3.1
load append "" 3 filter "[HOH]"
On Sun, Jun 23, 2013 at 11:59 PM, Robert Hanson <[email protected]> wrote:
> 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
>>
>>
>>
>> ------------------------------------------------------------------------------
>> This SF.net email is sponsored by Windows:
>>
>> Build for Windows Store.
>>
>> http://p.sf.net/sfu/windows-dev2dev
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>
>
>
> --
> 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
>
>
--
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
------------------------------------------------------------------------------
This SF.net email is sponsored by Windows:
Build for Windows Store.
http://p.sf.net/sfu/windows-dev2dev
_______________________________________________
Jmol-users mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/jmol-users
