hi all
sorry for asking non ccp4bb question.
i am trying to crystallise phosphatase protein,it has histag.I am getting very
tiny crystals into .1m hepes ph7.4,1m Na-K tartrate.I tried
additives(MPD,ethanol,propanol)for improvement of crystals,but didnt get any
success.I have tried both
Francis E Reyes schrieb:
Hi all
Can XDS take in additional images that have a different template name and reside
in a different directory? The reason is that I have high res images and then low res
images in different directories that I want XDS to consider.
Thanks!
FR
Hi Francis,
XDS
Hi folks, hope all is well with you on this sunny day (well it is sunny
over here!)
I am trying to recompile some code on a machine that does not have the
ifc compiler installed. (The code did compile w/o problems on another
computer that has ifc). It all works fine except for one program
Hi all,
Someone knows if ACORN2 (Acta D 2009, 881) is implemented in ccp4? If no,
where is possible to find a copy or when it is going to be implemented?
Thanks
Jose Otero
Spine 2-Complexes - Teach SG workshop:
Advanced Strategies for the Expression of Proteins and Protein Complexes in
Yeast
Barcelona, Spain. November 19-20, 2009
The workshop is aimed at advanced graduate students and postdoctoral fellows
and will deal with state-of-the-art technologies for the
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Atul,
Reasons could be so many. Since you say that the His-tag is still present in
your protein try to remove it and
Dear all,
I cannot get imosflm refining any cell, the program simply stalls: all
you have is the little E at the top right rotating, but no messages,
no errors, no crashes. 'Abort' doesn't have any effect either, nor it
has the sequence 'Pause'-'Continue'.
I have this problem with:
OS:
Dear Miguel,
You may find that replacing the ipmosflm binary with the one from
Harry's web page may be more reliable - typically these sorts of
things come down to gfortran or g77 being a little keen in
optimization.
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/
Cheers,
Graeme
2009/9/30 Miguel
Le 30 sept. 09 à 17:27, Graeme Winter a écrit :
Dear Miguel,
You may find that replacing the ipmosflm binary with the one from
Harry's web page may be more reliable - typically these sorts of
things come down to gfortran or g77 being a little keen in
optimization.
Dear all,
In the phaser .sol file what do the two LLG's correspond to on the
SOLU SET line eg
SOLU SET RFZ=20.7 TFZ=35.4 PAK=0 LLG=1699 LLG=2821
Do they show an initial and a refined LLG or do they correspond to the
rotation and translation function as in the Z scores?
I checked the
Hi,
I'm working with a 1.8 A structure with Coot and Refmac, and there are
many sidechain rotamers that show very clear difference density peaks
for setting their correct positions. However, Refmac continuously
moves the rotamers back into negative density peaks. It's really
quite
Dear Peter,
This simply should not be happening.
The actual value of the weight term btw does not say much, what we
would need to know is the resulting rmsd, or the associated z-score.
For what you describe, weighting should not matter really - same goes
for the torsion restraint, that will
A post-doctoral position is available in a virus structure laboratory.
Experience in macromolecular crystallography, electron microscopy,
molecular biology and protein chemistry is desirable. Please e-mail
applications to Michael Rossmann, _...@purdue.edu mailto:m...@purdue.edu_
(dept of
Dear All
Does anyone know a software or web-server which can predict potential
disulfide cross-linking sites?
I have solved a crystal structure. Is there a software to read in the
coordinates
file and symmetry information and predict the potential contacting
residues
which I can then mutate to
I remember this question (and the answer) from 11 years ago!
http://www.ysbl.york.ac.uk/ccp4bb/1998/msg00051.html
HTH
Peter
2009/9/30 Jie Liu j...@trimer.med.cornell.edu:
Dear All
Does anyone know a software or web-server which can predict potential
disulfide cross-linking sites?
I
Is it possible there are alternate conformations
for these side chains? Refmac, or any other refinement program, will
try to fill one of the density regions with your side chain, but
because of partial occupancy, a negative difference map will result,
with accompanying positive density in the
I think the second LLG value is after refinement. But sometimes I see that
the second LLG goes negative and I wonder what it means. For example:
RFZ=3.1 TFZ=17.2 PAK=0 LLG=238 LLG=-603
-Konstantin
On Wed, 30 Sep 2009, Simon Kolstoe wrote:
Dear all,
In the phaser .sol file what do the two
Hi Peter,
I think, instead of tightening the weighing term, giving it slight freedom
would have helped.
If data quality is good at 1.8 ang, then it certainly deserves more freedom.
What do you think.
best wishes
Manish
Manish Chandra Pathak, Ph.D.
Department of Biochemistry
Emory
Hi,
I have been using a dimer as a search model in MOLREP (there will be
several in AU),
for some reason the program tends to break the dimer into monomers
wihtout asking me..
how is this determined in the program... a more detailed manual would
be nice, also on the output
as the different
In a Phaser automated molecular replacement job, it does almost
everything at a working resolution and then a final refinement at a
final resolution. By default, the working resolution is 2.5A and the
final resolution is the full resolution of the data set. So the
second-last LLG is the
Posted on behalf of James G. Tobin, LLNL
Dear Colleagues,
It is with great sorrow that I must report that Peter Boyd has passed
away, in his sleep at home on Friday morning, September 25th. His
family is planning a private service.
If you wish, condolences can be sent to MaryBeth Boyd at
I am just wondering if anyone else is getting just a little bit peeved
that the BB is now primarily being used as a jobs board?
--
Dr. Christopher J. Law,
Queen's University Belfast
Hi Peter,
sorry for not answering exactly your question... but since this is
relevant I reply anyway:
The latest version of phenix.refine has an option fix_rotamers=true,
that automatically fixes all side chain rotamers by going
residue-by-residue and choosing the best one based on density
Le 30 sept. 09 à 22:07, Christopher Law a écrit :
I am just wondering if anyone else is getting just a little bit peeved
that the BB is now primarily being used as a jobs board?
--
Dr. Christopher J. Law,
Queen's University Belfast
Hi Christopher,
Well, I quote from the CCP4 web site:
I personally am not peeved at all, but I am getting concerned that most of
the jobs advertised are postdocs. Mighty and mysterious market forces have
cut very deep into the heart of structural science and this is not good.
Artem
Nothing is built on stone; all is built on sand, but we must
Dear Atul,
A question that any prudent structural biologist should ask sooner or later
once 'very tiny crystals' are obtained is - are these crystals made of my
protein of interest? I've witnessed at least three cases of 'tiny crystals'
being another (unintended) protein (confirmed by solving
At the risk of being the first job posting after the recent discussion,
please see the following link for job description:
http://www.structbio.pitt.edu/webusers/xray/
--
Laurie Betts
X-ray Crystallography Facility Manager
Department of Structural Biology
University of Pittsburgh
1050 BST3
3501
I always Look on the Bright Side of Life, so I take a certain solace in
the fact that while this may be true, most postdoc positions pay about as
well as my job, if not better.
On Wed, September 30, 2009 5:52 pm, Artem Evdokimov wrote:
I personally am not peeved at all, but I am getting
Are the salaries compared in orders of magnitude?
Or you mean other pays?
On Sep 30, 2009, at 8:30 PM, William Scott wrote:
I always Look on the Bright Side of Life, so I take a certain solace
in
the fact that while this may be true, most postdoc positions pay
about as
well as my job, if
Christopher,
I don't think you will have any more 'peeved' feelings when you ARE looking for
a job.
No, just California Dollars, which I think are on a par with those printed
in Zimbabwe prior to April 12th.
On Wed, September 30, 2009 8:27 pm, aaleshin wrote:
Are the salaries compared in orders of magnitude?
Or you mean other pays?
On Sep 30, 2009, at 8:30 PM, William Scott wrote:
I
Christopher,
I don't think you will have any more 'peeved' feelings when you ARE looking for
a job.
r
On Sep 30, 2009, at 1:07 PM, Christopher Law wrote:
I am just wondering if anyone else is getting just a little bit peeved
that the BB is now primarily being used as a jobs board?
I think the people looking for jobs have different feelings.
But using the CCP4BB as a gripe board, now there is
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