Hi,
what resolution range do you use? You can try reducing it a little.
How big is your cell?
Tim
On Friday 18 May 2007 13:46, Jay Thompson wrote:
> Hi,
>
> Thanks for the suggestions and quick reply. Suggestions work great!
>
> But I have another problem and looking back at the ccp4bb, I see t
Hi,
Thanks for the suggestions and quick reply. Suggestions work great!
But I have another problem and looking back at the ccp4bb, I see that Elenor
had a similar problem late last year. The error message is as follows:
--
OUT OF MEMORY ERROR: St9bad_alloc
--
Hello,
you could try to let phaser search for the first fragment, too. That way it
should produce a file ending with '.sol' which you can pass to phaser for the
second search (bottom at the ccp4-gui, "Define search sets...").
Otherwise, if you do not want to move the first fragment, both the Eu
What about giving the correctly positioned partial solution,
and fixed angles/translation of 0,0,0,0,0,0 for that part?
Jay Thompson wrote:
Hi,
I have a question with molecular replacement using Phaser. I'm trying
to solve a complex and I have a partial molecular replacement solution
solved
Hi,
at 1.2A resolution, you can probably go higher than 2 with the weighting term,
especially at the end of your refinement, when the model is near
completeness. You can try 'weight auto' to let refmac5 figure out the correct
weight (you have to use 'Run&View Com file' to edit the script manual
Hi,
I have a question with molecular replacement using Phaser. I'm trying to
solve a complex and I have a partial molecular replacement solution solved
using another program. This solution is correct and makes up ~50% of the
entire complex. I wanted to fix this solution and search for another
Dear all,
I am having a problem with refining my structure using
refmac5. Basically, I am trying to make some small
changes to several places on the backbone. But the
thing is that, after restrained refinement, the
changes I made would be all gone and the chain stayed
exactly where they were befor
Dear you all
I have a modified peptide. The N atom of the first Glycine is replaced
by
an C atom, and it makes covalent bonds to the N atom of the fourth
amino acid through a -C=C-C- linker. In case I didn't make it clear,
here is a simple illustration:
.(CO-Ca-C)-C=C-C-N (N belongs
Hi Mark,
Getting reliable stats straight from the PDB is nearly impossible. Waters
are commonly used to fill the gaps in difference maps, just to lower the
R-factor. Just look at the density for almost any structure. You'll see
that there are quite a few waters that have no density at all, insanel
The CCP4 program rwcontents includes the data from
Carugo & Bordo, Acta Cryst D, 55, 479 (1999)
Headline figures are 1.0 waters per protein residue at 2.0A, and 1.6-1.7
waters per protein residue at 1.0A. They use mainly room temperature,
but also some cryo structures.
And, as Clemens said, you s
There are still places available at the TeachSG Workshop:
Biological macromolecules and their ligands
Techniques in X-ray structure analysis and Docking
This workshop will be held from 10th -11th Jun 2007 in Prague.
The workshop is designed to give protein crystallographers good
background o
Hi Mark,
I attach a little plot based on a quick analysis of recent PDB entries
(between Jan 04 and Nov 06, only Xray). This shows the number of
waters (HOH residues) per ATOM record (i.e. mainly protein,
RNA/DNA). If you want the number of waters per amino-acid residue, you
could just multiply it
Forwarded on behalf of the organisers.
Alun
___
Alun Ashton, [EMAIL PROTECTED] Tel: +44 1235 778404
Data Acquisition Group, http://www.diamond.ac.uk/
Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.
-Original Messa
Hello everyone,
I would like to ask for any information on reasonable, preferably
quantitatively derived values for the approximate crystallographic
H2O to residue ratio versus resolution for protein structures ?
Any references or studies would be ideal, but rules of thumb
would also help. If th
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