Bump.

I have an S-methylcysteine sulfoxide so I downloaded it from WebCSD from the CCDC website. So far so good. Available in three formats but I wanted it to work as a modified residue so I followed the advice here. Opened it in PyMol, saved it as a pdb file and edited the atoms in a text editor to fit with a normal residue. But phenix.elbow doesn't treat sulfur correctly. The geometry is right but it adds an extra hydrogen to the sulfur and the oxygen - they should have a double bond instead. If I run phenix.elbow directly on the files downloaded from WebCSD I get the double bond but I also get a flat system; as if my sulfur was a carbon.

Yes, I tried --opt.

Attached the best results.

My phenix version is 1299.

tl;dr phenix.elbow fails at parameterising DMSO.

Help?

Cheers,

Morten

On 29 July 2012 04:41, Paul Emsley <paul.emsley@bioch.ox.ac.uk> wrote:

On 27/07/12 13:43, Schubert, Carsten [JRDUS] wrote:

What are the current best practices for modified aminoacids? I have a peptide with and N-terminal Acetyl-proline which I am trying to model. The initial approach was to locate the aminoacid in the chemical components dictionary (N7P) and replace the residue in coot.

do the restraints specify that N7P is a non-polymer (in which case coot will treat it as such) or as an L-peptide?

Unfortunately the link to the next residue is not recognized, so the residue is just floating about.

Doesn't sound very much like how a L-peptide should behave to me...

Paul.

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--
Morten K Gr�ftehauge, PhD�

Pohl Group

Durham University