Dear all,
Is there any CCP4 module/ other software/ web server which can
determine which particular residues form the surface of a pocket/ binding-site
in a protein?
Thanks in advance,
sreetama
On 10/04/2012 04:09 PM, sreetama das wrote:
Dear all,
Is there any CCP4 module/ other software/ web server
which can determine which particular residues form the surface of a
pocket/ binding-site in a protein?
Do you mean "residues not far from any ligand atom"?
And you know wher
Dear Peter,
my guess is that isopropanol might have evaporated and, in general, that the
concentration of PEG4000
might be higher that in the starting solution because of evaporation.
I would try to decrease the isopropanol concentration, or even eliminate it.
As a "cooker test" if you sm
Try PISA
-- Eugene
On 4 Oct 2012, at 08:09, sreetama das wrote:
Dear all,
Is there any CCP4 module/ other software/ web server which can
determine which particular residues form the surface of a pocket/ binding-site
in a protein?
Thanks in advance,
sreetama
--
Scanned by iCr
You can also try the CASTP server
On Thu, Oct 4, 2012 at 2:47 PM, wrote:
> Try PISA
>
> -- Eugene
>
> On 4 Oct 2012, at 08:09, sreetama das wrote:
>
> Dear all,
> Is there any CCP4 module/ other software/ web server which
> can determine which particular residues form the sur
Dear All,
A 1 year position has become available for a Research Associate in the Membrane
Protein Laboratory (MPL) for crystallisation, crystallographic and structure
determination of a bacterial antibiotic transporter. The successful candidate
will work on improving the crystals and solving th
Apologies for revisiting this topic but I wanted to post a summary of the
responses for the compulsive archive searchers like me.
Several people suggested the addition of ATP (5 mM) to the buffers either
at lysis or once the protein is bound to the column (see ref: R. E. Joseph;
A. H. Andreotti, P
Hello everyone,
I would like to share my experience with one dataset and request some
advice on which is the best way to prove a conformational change seen in a
density map.
The first issue arose when we were looking for an extra ribosomal factor
added to a crystalized ribosome. After careful dat
Try GraphEnt but you might have to recompile it for your size of proteins. That
has helped me several times to see something that was barely there.
Here's the link for the 'click-generation':
http://utopia.duth.gr/~glykos/graphent.html
Jürgen
..
Jürgen Bosch
Johns Hopkins Un
I am very sorry to hear the sad news. Like innumerable others, I am very
grateful to have had the opportunity to meet "The Prof. Johnson" of the
classic Blundell & Johnson crystallography textbook. I met Prof. Johnson at
Diamond a few years ago and immediately saw in her an inspiring, graceful
and
Dear Israel,
I wonder why you do not see anything in your Fo-Fc (mFo-DFc?) maps,
since the limit for a (n+1) * mFo - n * DFc map, when n approaches
inifinity, is the mFo-DFc difference map. There is nothing wrong in
going further like with 4mFo-3DFc maps, but you should bear in mind that
they are
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