[phenixbb] Best practices for modified aminoacids

Nigel Moriarty nwmoriarty at lbl.gov
Tue Mar 5 13:41:12 PST 2013


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.



On Tue, Mar 5, 2013 at 6:16 AM, Morten Groftehauge <
mortengroftehauge.work at gmail.com> 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 <paul.emsley at 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 Grøftehauge, PhD
> Pohl Group
> Durham University
> _______________________________________________
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> phenixbb at phenix-online.org
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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