Dear all,
Is there a program or server that would define a ellipsoid around a
given protein molecule? I would also like to calculate the axis components
of the defined ellipse. Thanks in advance..
cheers,
wandu
Hi Xu,
Curves+ (http://gbio-pbil.ibcp.fr/Curves_plus/Curves+.html) can generate
helical axis of DNA.
Wataru
On 2011/05/28, at 7:51, xu xiang wrote:
> Hi all,
>
> Sorry for this off-topic question. Does anyone know how to generate or
> display DNA central axis? I want to measure the distance
Hi all,
Sorry for this off-topic question. Does anyone know how to generate or display
DNA central axis? I want to measure the distance between my protein and the
central axis.
Best,
Sean
Hi all
I was just fiddling around with ncs and maps, so I tried to use
maprot a 2fofc map (refined model) of a crystal that has two
molecules related by the NCS:
(given by LSQKAB over the CA's)
CROWTHER (Euler) ALPHA BETA GAMMA 95.8381478.49123 145.66571
TRANSLATION VECTOR
Hi Pascal,
The GST helps a lot with expression, but unfortunately it's very difficult
to purify it away after cleavage. I would strongly recommended to try MBP
tag.
Good luck!
Anna
On Fri, May 27, 2011 at 1:50 PM, Pascal Egea wrote:
>
> Dear All,
>
> This is not strictly a crystallography rel
Dear All,
This is not strictly a crystallography related question.
We are trying to express several membrane proteins and were considering the
use of GST as a fusion partner instead of the HIS or FLAG purification tags.
I would like to know if anyone had any experience (positive or negative) to
sh
There has been a serious problem in Refmac which apparently Garib
has fixed in this new release. When calculating structure factors
for models in space group P1 Refmac would "lose" some of the atoms.
I first ran into the problem by looking at the Electron Density
Server map for entry 3LEN.
Dear Xavier,
I am very sorry that I didn't respond instantly to your query about
this strange observation at the beginning of the month. After that, it was
sitting rather invisibly in my mailbox, given that its subject line said
"Re: [ccp4bb] Dehydration treatments" :-) .
We are just ab
Dear all,
We have a Digilab Honeybee96 pipetting robot with a few broken needles
in the lab. I have got replacement needles from Digilab but their
alignment tools are on backorder. Does anybody (preferably nearby) have
these tools and would be willing to lend them to us? We would pay for
shipping a
Dear CCP4ler,
I have a strange fortran error attached below when I started a restrained
refinement with Refmac. I tried also for the beginning a simple rigid body
refinmet for comparison and except that it complains about the Hessian B Array,
which ist too big, it runs to completion.
Has anyone
Hi Jerry -
By AUC, do you mean sedimentation velocity (SV)?
Both gel filtration and SV are not terribly great ways to determine precise
molecular mass, especially if the macromolecule of interest is anisotropic
in shape. In your SV values, do you see a large f/fo, or a broad
distributio
Afshan
Radaev and Sun published a paper a few years ago showing that
crystallization conditions for complexes are strongly biased towards PEG
conditions (rather than e.g. high salt conditions). The reference is below.
I would use microseeding into random screens [2], using the crystals that
you
Another reference with a detailed method for transferring crystals to new
conditions prior to soaking is
Ray WJ Jr, Bolin JT, Puvathingal JM, Minor W, Liu YW, Muchmore SW. Removal of
salt from a salt-induced protein crystal without cross-linking. Preliminary
examination of "desalted" crystals of
Dear ALL;
I am sorry for this off-topic question about analytic ultracentrifugation
(AUC).
We recently solved one structure from crystals grown out of PEG4000 plus
buffer. Since the crystal was grown from PEG, we think the protein would
maintain its native oligomerization state as in
Job Title: Postdoctoral Research Associate - Protein Crystallography,
Macromolecular Single-Crystal Spectroscopy, X-ray Diffraction
Job ID: 15788
To apply, please visit: http://www.bnl.gov/HR/careers/
Requires a Ph.D. in biochemistry, chemistry, biology, biophysics, or
related areas, and s
Dear Afshan,
As Fred suggested, you may try to get rid of the ammonium phosphate by
transferring it to a PEG solution. However, it may be that you get the nice
crystals because your protein is stabilized by the phosphate in the active
site. Crystal packing may prevent the phosphate from leavin
Hi all,
This may be of interest to those methods developers amongst us who are ogling
the rich potential bounties to be reaped by applying low-resolution X-ray
model-building and refinement methods to EM maps...
--Gerard
-- Forwarded message --
Date: Thu, 12 May 2011 07:52:48
Afshan Begum wrote:
Dear All,
I have a severe prob lam to performed my ligand binding study with
corresponding protein. I have taking the native diffraction data at
1.75 A and after that i have performed soaking as well
co-crystallization experiment with my inhibitors.
Problem is that at the
Dear All,
I have a severe prob lam to performed my ligand binding study with
corresponding protein. I have taking the native diffraction data at 1.75 A and
after that i have performed soaking as well co-crystallization experiment with
my inhibitors.
Problem is that at the active site phosphate
Dear colleagues,
Q2 is solved by new installation of Refmac. Many thanks for your time
and effort. I appreciate all your comments.
Petr
2011/5/27 David Cobessi :
> Dear Petr,
> Before running Refmac, you have to remove the ANISOU line using pdbset for
> example. In fact you should not add the T
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A postdoctoral research scientist position is available in the Wellcome Trust
Centre in the University of Oxford, UK. The post is funded for 3 years
Salary range £29,099 to £35,788 p.a (approximately 33,-41,000 Euros)
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Dear Petr
Newer version of refmac is 5.6 and it should be available from ccp4 soon.
Meanwhile you can try this version from this website
http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.6_linux.tar.gz
There are versions for mac etc also.
regards and I hope you will sort it
Dear colleagues,
regarding Q2:
I do not use TLS parameters, the space group is P1, and yesterday I
tried to refine the structure with anisotropic ADP (60,000 reflections
against 50,000 parameters) - no positive maximums. Then I used the
anisotropic model as input and refined isotropically, the ma
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