[phenixbb] Ligand restraints editing with REEL

Ralf W. Grosse-Kunstleve rwgk at yahoo.com
Sat Sep 18 08:13:41 PDT 2010

Hi Joe,
Nigel who wrote elbow+reel is traveling so I'll try to help until he gets a 
chance to respond.
I very simple suggestion is do manually edit the cif file generated by elbow 
before you
pass it to phenix.refine; The cif file format is meant to be human-readable.
Another option is to modify the dihedral definitions in reel and to save the 
file without
running the elbow optimizations again. There is nothing wrong with overriding 
elbow results with your chemical knowledge.
A third idea is to run elbow with the Glutathione from your PDB file as the 
input, instead
of using the smiles string. That may give elbow a better start.
If phenix.refine rejects your inputs I'd be interested to see the log file with 
the error messages.
If you send me the Glutathione residue from your PDB file (directly; not to 
list) I could help more.

From: Joseph Brock <joeylives2ride at hotmail.com>
To: phenixbb at phenix-online.org
Sent: Sat, September 18, 2010 1:09:23 AM
Subject: [phenixbb] Ligand restraints editing with REEL

 Hi all,

I'm working on a 1.5A structure that contains a novel ligand within the active 
site, which is an Arsenic derivative of Glutathione, using the Phenix GUI, 
version 1.6.4-486. 

I have been using the 'Molinspiration' webpage 
(http://www.molinspiration.com/docu/webme/) to generate a smiles string, which I 
then feed into ELBOW. Although the structure/chemical restraints of Glutathione 
should be unchanged by the covalent linkage to arsenic through the cysteinyl 
sulfur, the resulting restraints file consistently restricts one of the 
dihedrals to a value that is incompatible with the (quite clear) electron 
density. This occurs regardless of wether i use AM1 optimization, and is 
unresponsive to using native Glutathione (which refines into the corresponding 
density extremely well) as an input geometry file with any of the available 'Use 
geometry for' options (final geometry, initial geometry, etc).

I then tried opening the output file in REEL and manually changing the 
corresponding dihedrals to those of glutathione, however after running simple 
optimization, the resulting restraints file has the same problem, and upon 
choosing the 'transer geometry and restraints' option (or any option) midway 
through running the 'eLBOW optimization' or 'AM1 optimization' options, Phenix 
consistently crashes.

Any advice on how to transfer the origional geometry of native Glutathione to my 
new ligand effectively would be greatly appreciated. I'm a little confused as to 
the abilities of REEL, and how to affect them.

Thanks so much in advance.


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