Dear Nazia,
you give very little details, so it is difficult to give a specific advice.
Here are some comments:
-How high is your Rfree? Depending on the resolution of your data, an Rfree in
the 25-30% range while not good, may still be acceptable.
-Are there problems like ice-rings in your
Dear Jens,
did you try aimless instead of scala? I understood it is the successor
of scala and I would not have thought scala is still being developed.
Phil should correct me if I am wrong.
Best,
Tim
P.S.: I hope it will be a long time before the last release of ccp4. ;-)
On 12/10/2013 05:05
Dear Jens
I'm surprised by this as Scala hasn't changed for quite a long time, as it is
now now superseded by Aimless. However, I haven't implemented a reference
dataset in Aimless since in the end I decided that it wasn't very useful, so if
you find it useful then you will indeed need to use
Dear Careina,
you can also apply for beamtime at PETRA-III. You get away with the same
size crystals but only require a nano liter drop rather than a few ml of
your sample. And you probably get beamtime much quicker because all the
equipment is installed and collecting a data set takes very short
Yes, Tim is right… for now… in few years, with the E-XFEL, we'll get to much
less sample, and much more time available. But that's in few years.
Leo
On Dec 10, 2013, at 10:01 AM, Tim Gruene t...@shelx.uni-ac.gwdg.de wrote:
Dear Careina,
you can also apply for beamtime at PETRA-III. You get
Dear Nazia Nasir,
it is important to know what you do BETWEEN the refinement cycles. Rfree
not moving and R1 dropping is often a sign of overfitting, i.e. you
might be adding water molecules into the noise or refine the occupancy
of single atoms, e.g. in a ligand or of the water molecules.
As a
'Will' is a fashionable word - but since even a Nobel prize was given
based on promises never kept, who would be surprised...
Best wishes from now,
Tim
On 12/10/2013 10:11 AM, CHAVAS Leonard wrote:
Yes, Tim is right… for now… in few years, with the E-XFEL, we'll get to much
less sample, and
Indeed nothing is predictable. We can only assume things on what is *planed*
and *promised*, and you can take my words on the fact that I will do my best to
have it done properly and as close to the expectations as possible. But again,
nobody can really predict the future.
Finger crossed.
Dear colleagues,
A PhD position is available in (membrane) protein biochemistry and X-ray
crystallography in the newly established research group of Dr. Henning Tidow at
the Institute for Biochemistry and Molecular Biology, University of Hamburg,
Germany.
Our group studies the
Well the density strongly suggests a Tryptophan side chain.
Sometimes discrepancies (errors) appear in sequences. How certain are
you of the accuracy of your sequence?
HTH,
Fred.
On 10/12/13 13:44, PriyankMaindola wrote:
dear members
i am trying to solve this crystal structure but
I am
check an anomalous map!
The obvious thing to do to rule out gold binding
-
Dr. Matthias Zebisch
Division of Structural Biology,
Wellcome Trust Centre for Human Genetics,
University of Oxford,
Roosevelt Drive,
Oxford OX3 7BN, UK
Phone (+44) 1865 287549;
Dear colleagues,
below is an advert for an postdoc position in my group.
best, Marko
Applications are invited from post-doctoral scientists with expertise in protein
crystallography to join the group of Dr Marko Hyvonen
(http://www-cryst.bioc.cam.ac.uk/groups/hyvonen/) at the Department of
My first guess was also a metal ion. However, a tryptophan as Fred suggested
cannot be ruled out. A simple preliminary test is to scroll up the contouring
level and look when the contours of the blob disappear. If the contours quickly
disappear, you have something disordered or light. If the
Hi all,
I was wondering if anyone had seen this behaviour with Coot.
Whatever version I was using, or the latest that comes with ccp4 now
gives me the following error message. Rather cryptic message for me.
Thanks,
Fred.
The program 'coot-real' received an X Window System error.
This
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Fred,
without further info my guess is that you try to run coot through
X11-forwarding of an ssh-connection which sometimes causes this error
message, or you need to recompile your graphics driver, e.g. because
your kernel was updated and the
Hi,
The current rwork is 0.31 and Rfree is 0.4, after 10 sets of
refinement. I build quite a large portion before sending it for
refinement.
Thanks a lot for all the answers. I have started working as per suggestions.
--
Nazia Nasir
PhD Scholar
Protein Crystallography Lab
National Institute of
Hi Nazia,
you did not say what Rwork and Rfree values are... If, for instance,
Rwork=20% and Rfree=21% then a situation when Rfree stays the same or even
increases and Rwork goes down is totally valid as long as a reasonable
Rfree-Rwork gap is maintained.
The point is that you need to look at
It doesn't look like you left a CN on your gold atom. These things
are pretty much covalently bound.
Dale Tronrud
On 12/10/2013 08:13 AM, PriyankMaindola wrote:
dear all:
I. i am not able to fit trp,
since
1. trp doesnt fit well
2. positive density comes in fo-fc map after refinement
Hi,
David Waterman and Andrey Lebedev sorted out my problem with Phaser log file
output in QtRView on Windows.
It turns out that Phaser on Windows fails to write a User: line just under
the program banner in the log. This line is necessary for proper processing of
the log file. You can
Priyank,
I think it's too far out from the Calpha to be Trp, and also not quite
flat enough. The map contains more information than just the shape as
to identity. Compare the max peak height of the 2Fo-Fc blob near the
Gln to neighboring element heights.
Much higher than C/N/O ? Probably
Yes, a bugfix from the phaser code side has been committed to the phaser
svn. Airlie
On Dec 10 2013, Derek Logan wrote:
Hi,
David Waterman and Andrey Lebedev sorted out my problem with Phaser log
file output in QtRView on Windows.
It turns out that Phaser on Windows fails to write a User:
--
Ved Prakash Dubey
Graduate Student (SRF)
Centre for Cellualar Molecular Biology
S-210 (C.C.M.B.) Habsiguda Uppal Road
Hyderabad (A.P.) 57
09395198575
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