Dear Afshan,
From your question it is not completely clear where your problem lies.
However, I assume you have soaked/cocrystallized your protein (crystal)
with a ligand and collected a data set and want to know whether or not
your ligand has bound.
In that case I would do a few cycles of
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Dear all,
I tried MolRep with a two domain protein. I have cut the two domain as one
domain rotates which prevent a search with the complete model. After I finished
the first run. I put this solution as fixed input model in the second molrep
run
with the second domain. The resulting solution
http://www.ysbl.york.ac.uk/~alexei/molrep.html#stick
On Thu, 2011-02-17 at 19:32 +0100, Christian Roth wrote:
Dear all,
I tried MolRep with a two domain protein. I have cut the two domain as one
domain rotates which prevent a search with the complete model. After I
finished
the first
Dear all,
We are working on a Category 3 protein which must be contained so we have
our crystals mounted in a loop and then covered with a plastic Mitegen
cover which is glued in place. We're currently collecting at room
temperature, but wondered if anyone has any experience of using a
The molecular replacement program does not know about your molecule
being a single polypeptide chain. The problem is fit two bodies
therefore the program fits two bodies. The centre of mass of whatever
you wish to position is placed the standard asymmetric unit used by
the program. If it
Posted on behalf of Simon Hettrick, The Software Sustainability Institute:
If you want to use software to advance your research, the Collaborations
Workshop (CW11) on 3-4 March 2011 is the perfect opportunity to meet the
researchers, software developers, funders and other software experts that
How low? Back in the old days when we mounted xtals in capillaries, you could
sometimes see significant reduction in radiation damage by data collection
temperature from room temp to ca. 0 deg C (zero is generally safe, since the
PEGS/salts in your mother liquor will depress the freezing
It was my understanding that Mitegen plastic capillaries only work for
crystal evaluation, since they are permeable enough to cause crystal to
dry up within few hours - hopefully that is enoug time to get a complete
dataset, but one should be concerned about changes in unit cell
parameters as
Dear CCP4 and XDS users,
I have a P21 case with some strange ratios in the cell dimensions : a, b=a,
c=1.5a, 90, 105, 90. The native patterson shows a strong peak (40% of
origin) at (x,0.5,0) indicating some pseudo symmetry. Such cell dimension
and peak prompted me to think that the actual space
To my fellow scientists,
If you use the US National Laboratories or facilities, please take 5 minutes of
your time now to tell your congressmen/women about it - why the facilities are
important to your research and why your work is important. As scientists, we
don't often communicate the
Mitegen plastic capillaries can actually last about a week from a
Mitegen seminar I attended. I also got ice when I tried to freeze it
once and I didn't further pursue it. Maybe coat the capillary with
glycerol will help?
Nian Huang, Ph.D.
UT Southwestern Medical Center
On Thu, Feb 17, 2011 at
Dear CCP4 mailing list
I have a relatively simple question. How do I get sequence file in .pir format
which is required for many programs? I normally use fasta format but some
programs eg arpwarp do not allow me to use that
Thanks for your help
Careina
Hi Careina,
just change extension of your sequence file, i.e.:
change yoursequencefile.extension (where extension could be .txt
.fasta, etc) to yoursequencefile.pir
It should work then.
Cheers,
Albert
Albert GUSKOV (Dr) | Research Fellow | Division of Structural
Computational Biology | Nanyang
Hi Careina,
There are several places on the web that describe the
PIR format (also called NBRF) E.g.
http://www.ebi.ac.uk/help/formats.html#pir
http://www.bioinformatics.nl/tools/crab_pir.html
etc.
The program readseq -- either via command line or
webserver -- e.g.
On 02/17/2011 09:35 PM, Peter Grey wrote:
Dear CCP4 and XDS users,
I have a P21 case with some strange ratios in the cell dimensions : a, b=a,
c=1.5a, 90, 105, 90. The native patterson shows a strong peak (40% of
origin) at (x,0.5,0) indicating some pseudo symmetry. Such cell dimension
and
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