Hi Jason and Troels
    Thanks for your suggestions, but removing the alternate conformation doesnt solve the problem in itself.  I have already played around with removing the alternate conformation using the alt selection method, and the only way successfull is to delete the alternate conformation from the PDB file, then reload it into Pymol. Pymol doesnt initialise the backbone bond order or something, when theres an alternate conformation, and is thus not able to assign the correct hydrogens, even after the alternate conformation has been deleted.

Heres an example of an updated script with problems.
fetch 1zw9
zoom resi 12
remove not alt ''+'A'
h_add 1zw9

Look at the hydrogen at the backbone nitrogen of resi 12 and carbonyl carbon at resi 11.

whereas this hackish script works

fetch 1zw9
remove not alt ''+'A'
save temp.pdb, 1zw9
delete 1zw9
load temp.pdb, 1zw9
h_add 1zw9
zoom resi 12

Is there a command to get PyMOL to reparse the structure after removing the alternate conformations?

Best Regards
Esben Jannik Bjerrum

From: Jason Vertrees <jason.vertrees@schrodinger.com>
To: Esben Jannik Bjerrum <EsbenJannik@rocketmail.com>
Cc: "pymol-users@lists.sourceforge.net" <pymol-users@lists.sourceforge.net>
Sent: Friday, April 19, 2013 6:43 PM
Subject: Re: [PyMOL] Problems with H_add when theres alternate conformations present

Hi Esben,

It's up to you to decide how you want to handle this. You have a few options.

You can remove unwanted alternate conformations, for example:

remove not alt ''+'A'

then run your script.

Or you can specify PyMOL only add hydrogens to a certain set of conformations:

# only h_add to alt conformations labeled 'C'

h_add 1zw9 and alt 'C'

To only add hydrogens to default or 'A' conformers do the following:

h_add 1zw9 and alt ''+'A'


-- Jason

On Thu, Apr 18, 2013 at 3:59 AM, Esben Jannik Bjerrum
<esbenjannik@rocketmail.com> wrote:
> Hi Pymol Users
>    I have a problem with wrong atom assignment, and subsequently wrong
> addition of hydrogens, if theres alternate conformations present. I hope
> anyone else has experience with this or suggestions for troubleshooting.
>    I have developed some scripts that downloads pdb-files from a list, add
> hydrogens to them, and otherwise prepares them for further usage. However,
> if theres alternate conformations present, the atoms on the backbone gets a
> wrong charge assignemt or something, breaking the subsequent addition of
> hydrogens. It seems to happen at PDB load time.
> Example steps to reproduce
> fetch 1zw9
> zoom resi 12
> h_add 1zw9
> the hydrogen on the nitrogen in the backbone peptide bond doesn't make a
> planer configuration, and if I save the object, the oxygen is assigned a -1
> charge. This makes troubles in my subsequent workflow.
> I've tried to delete the alternate conformations inside PyMOL before adding
> hydrogens, but that doesnt fix the problem. I can fix the problem by
> removing the alternate conformations from the PDB file before I load it into
> pymol, but I would rather fix it inside pymol in my scripts.
> Best Regards
> Esben Jannik Bjerrum
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Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

(e) Jason.Vertrees@schrodinger.com
(o) +1 (603) 374-7120