[ccp4bb] MSE and Refinement

2008-03-25 Thread Kim, Eun Young
Hi all, I have a question about registering Se. Since diffraction quality of my SeMet dataset is better than a native one, I want to use a SeMet dataset (collected at a remote wavelength) for a final model while I am trying to get a decent native dataset. I tried to put MSE in some MET positio

Re: [ccp4bb] MSE

2007-08-30 Thread Charlie Bond
Kim Henrick wrote: A standard amino acid is a gene product with a specific t-RNA. Isn't it arguable that Met-tRNA is no more specific for S-Met than for Se-Met, it's just a matter of what the organism has been eating? Cheers, Charlie -- Charlie Bond Professorial Fellow University of Western

Re: [ccp4bb] MSE

2007-08-30 Thread Kim Henrick
The PDB is not an isolated database and one of our tasks is to allow mapping and integration activities with other databases. The PDB has closely matched GENBANK and UniProt/SwissProt over the definitions of standard groups. A standard amino acid is a gene product with a specific t-RNA. The number

Re: [ccp4bb] MSE

2007-08-30 Thread P.Artymiuk
Phil If MSE were described with ATOM cards then rasmol and other graphics programs would display it in a sensible manner. This would be contrary to wwPDB policy which is to make coordinates C++-friendly rather than human-useable. Pete Pete Artymiuk Quoting Phil Evans <[EMAIL PROTECTED]>: > > A

Re: [ccp4bb] MSE

2007-08-30 Thread Joe Krahn
One more comment on MSE: Does anyone know why MSE was defined without a 'delta' on the selenium? Isn't that obviously wrong? Selenium-delta should be "SED ", just like S-delta is " SD ", so it can't be left off just because selenium is not a carbon. Phil Evans wrote: > > As an aside, does anyone

Re: [ccp4bb] MSE

2007-08-30 Thread Marko Hyvonen
> > % egrep '^CRYST|^SCALE|^ATOM|^HETATM.{11}(MSE|PTR|SEP|TPO)' your.pdb > > standard_residues_only.pdb I think the original request was to extract particular chains, so extending the above further to select (say) chain A egrep '^CRYST|^SCALE|^ATOM.{17}A |^HETATM.{11}(MSE|PTR|SEP|TPO) A' your.p

Re: [ccp4bb] MSE

2007-08-30 Thread Joe Krahn
The problem is that HETATM does NOT mean it is not an amino or nucleic acid. HETATM is used to describe "non-standard" groups, where the definition of "standard" means it is from a list of pre-determined, hard-wired residues with reserved names. It just happens that the list of selected "standard"

Re: [ccp4bb] MSE

2007-08-30 Thread Ian Tickle
Phil, Now you've opened this can of worms I'd like to add phosphoserine, phosphothreonine & phosphotyrosine to the wish-list of things that look like amino-acids to me. So to extend Clemens' suggestion to cover all these: % egrep '^CRYST|^SCALE|^ATOM|^HETATM.{11}(MSE|PTR|SEP|TPO)' your.pdb > sta

[ccp4bb] MSE

2007-08-30 Thread Phil Evans
As an aside, does anyone understand why MSE is not an amino-acid? Phil On 30 Aug 2007, at 15:31, Clemens Vonrhein wrote: If your PDB file conforms to standard http://www.wwpdb.org/documentation/format23/sect9.html#ATOM you could do % egrep "^CRYST|^SCALE|^ATOM" your.pdb > standard_resi