sential that we be part of the decision making process.
I just sent the following letter to the wwPDB, which is where
comments about the new format are supposed to go. If you will be at the
ACA meeting, I encourage you to complain lou
Eric Pettersen wrote:
> On Jul 21, 2007, at 11:12 AM, Joe Krahn wrote:
>
>> Another problem is that the original meaning of HET groups continues to
>> be corrupted. ATOM records are for commonly occurring residues from a
>> list of standard residues.
>
> No,
ke our own OpenPDB format?
Joe Krahn
o open-ended, depending on how the schema is managed.
I would be much more willing to work toward switching to mmCIF if RCSB
showed more interest in collaborating with the user community. If we
can't even get involvement in something as simple as the PDB format, why
should we think working with mmCIF will be any better?
Joe Krahn
manage all sorts of new
structural data is far from trivial. All I ask is that the file formats
and data schemas which we all have to use be considered public
standards, and not just for their own internal database design.
Joe Krahn
eement, it could be used as a community tool to
put together a draft revision of the next PDB format. With any luck,
some RCSB or wwPDB people would participate as well.
Joe Krahn
PDB Format Wiki, running on my home computer, at
http://pdb.homeunix.org. If it gains interest, I will see about moving
it to a proper Internet host.
Joe Krahn
Miller, Mitchell D. wrote:
> Hi Boaz,
> We were informed by an RCSB annotator in April 2006 that the
> RCSB had suspended i
th along one
direction that it allows the crystal to be well-ordered.
Joe Krahn
Jenny Martin wrote:
> I've been reading the contributions on this topic with much interest.
> It's been very timely in that I've been giving 3rd year u/g lectures on
> protein X-ray structures
than anything else,
and would help avoid the misunderstanding that so many people have about
the purpose of HETATM.
Joe Krahn
Phil Evans wrote:
>
> As an aside, does anyone understand why MSE is not an amino-acid?
> Phil
>
>
> On 30 Aug 2007, at 15:31, Clemens Vonrhein wrote
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
In general, it requires a LINK record to add the required bond. I don't
know how to set up refinement parameters. I had a similar case once (see
1ECC), and created a big non-standard residue containing both the amino
acid and ligand as one residue. (But, that was done in X-PLOR.) If
setting up link
I was using X-PLOR at the time. I later switched to a PRESidue patch. I
was not sure how many atoms must be added to a residue before a modified
amino acid becomes a linked amino acid. The PDB seems a bit adverse to
non-standard links. For example, why is NADP not two residues with a
LINK? There ar
room. Even then, I used
saturating ligand concentrations.
Joe Krahn
Nian Huang wrote:
> Dear All,
>
> I have been trying to get a protein-ligand complex crystal for a long
> time. Here, ligand is either substrate or product for this kinase. I
> have tried many methods: soaking with
are very common in crystallization trials. Maybe it would be useful to
tabulate common salt crystals to help guide optimization experiments.
Has anyone else tried to use salt crystal information beyond ensuring
that it is not protein?
Joe Krahn
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