Re: [phenixbb] Best practices for modified aminoacids

Morten It is always best not to use the PDB format as input if another is available as it suffers from a number of limitations. However, I am surprised that the other formats didn't provide a better result. I'd be interested in the 3 files you downloaded. To solve your problem, one of the best ways to get restraints is with the help of the Chemical Components. Your ligand, CYM, is specified by the PDB and you can use eLBOW to create a restraints file. phenix.elbow --chemical-component=cym and its available in the GUI also. Cheers Nigel On Tue, Mar 5, 2013 at 6:16 AM, Morten Groftehauge < [email protected]> wrote:

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 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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