Hi all, I just wanted to post a quick summary of how my problem was resolved. I later realised that the 'native glutahione' molecule I was transferring ligand restraints from was actually produced by eLBOW released under the Phenix package v1.4, and was therefore defined differently to those restraints created by v1.6.4-486. I was advised by Nigel (author of eLBOW and REEL) to download the latest nightly build (dev-541) and create a clean subdirectory. Copying my model.pdb and data.mtz file into this, running phenix.ready_set on these files and running phenix.refine with the resulting .pdb and .cif files, resulted in a ligand that was correctly restrained to refine into the density extremely well. Hope this is of help to anyone with a similar problem. Cheers, Joe.

From: [email protected] Subject: phenixbb Digest, Vol 58, Issue 18 To: [email protected] Date: Sat, 18 Sep 2010 12:00:01 -0700

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Today's Topics:

1. Ligand restraints editing with REEL (Joseph Brock) 2. Re: Ligand restraints editing with REEL (Ralf W. Grosse-Kunstleve) 3. Resolve NCS masks (Florian Schmitzberger)

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Message: 1 Date: Sat, 18 Sep 2010 08:09:23 +0000 From: Joseph Brock To: Subject: [phenixbb] Ligand restraints editing with REEL Message-ID: Content-Type: text/plain; charset="iso-8859-1"

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.

Cheers,

-Joe.