Thanks, valence guess was the key :-)
This makes sense, valence/bond assignment is run once the PDB is loaded, but
unfortunately fails with the alternate conformations. Removing the alternate
conformation doesnt update the bond information, making the save/reload of the
structure or valence gue
----
> From: Jason Vertrees
> To: Esben Jannik Bjerrum
> Cc: "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'
l-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 conformati
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
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
