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
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
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
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
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
>
> % 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
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"
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
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