Hello Everyone,
I have a question about getting rid of model bias in refinement with refmac. I
solved the structure with molecular replacement. After final refinement of the
structure, I found out some key amino acids in the structure and wanted to make
sure their conformations are correct. I
Postdoctoral positions available immediately in a membrane transport and
structural biology laboratory. Our new laboratory in the Department of Cell
Physiology and Molecular Biophysics at Texas Tech University Health Science
Center at Lubbock is well equipped with the state-of the-art equipmen
Those colorful tags may be too big for crystallization purpose. You can try
GFP or heme based tags. A few companies are promoting heme based red tags.
Red color is not very intense. You'd be better off with UV or GFP. There are
small molecule tags that links to Cys. But you'll spend a fortune to ge
Hi all,
I am curious whether there is an expression system in which the target protein
will be expressed with a tag, which has a strong extinction coefficient in
visible wavelength range? That will dramatically simplify my protein
purification and crystallization.
Thanks for your suggestion.
P K wrote:
I am new to the filed of crystallography. I am having trouble figuring
out what exactly does sigma level of electron density map mean.
When sigma level of a map is increased (say from 1.5 sigma to 2 sigma)
why the map covering individual residues becomes less wide and more
"precise
I am new to the filed of crystallography. I am having trouble figuring out
what exactly does sigma level of electron density map mean.
When sigma level of a map is increased (say from 1.5 sigma to 2 sigma) why
the map covering individual residues becomes less wide and more "precise"?
Shouldn't it
Dear Mark, thanks for your answer!
Yes, there is an actual change in energy and I guess my problem does not
have a single source!
In the case you know someone who faced/have faced a similar problem
around please tell me.
Brazilian regards,
LS.
1. Is the energy drift a change in flux or actual
A start is made, if somebody would like to comment / add information
to the open "?" that would be great.
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Synchrotrons
Jürgen
-
Jürgen Bosch
University of Washington
Dept. of Biochemistry, K-426
1705 NE Pacific Street
Seattle, WA 981
Hey Andrew! Thanks for answering!
Does someone have experience in minimize energy instabilities in
beamlines?
Are you sure it's an energy instability and not an intensity one?
It's quite rare to see energy instabilities from a well calibrated
monochromator. All monochromators should be in a clos
From: Ta Hai
Sent: Sat 7/26/2008 3:00 AM
To: Sampath Natarajan
Subject: RE: [ccp4bb] Refinement problem
With the R and freeR factor 45.3% and 51.4%, I'm quite sure that your MR
solution is not correct. Although your current model seems fitting with the
map, but it's just the biased map after re
You may need to consider (assuming that space group is correct)
1) Twinning. In this case even wrong solution at the early stages
would give lower Rfactor and at the later stages higher Rfactor
without accounting for twinning
2) Pseudo translation. In this case the solution could be in wrong
Hi Sampath,
You are asking many questions at once. Since I am right now trying to solve a
very difficult Se-Met structure, here are some ideas:
- Do you have an energy scan on your crystal, showing that there is absorbance
at the correct wavelength for Se? If yes, you have proof that there was
Dear All:
I have a peculiar problem with baculovirus expression of my protein. The
native protein elutes in Tris gradient. This has no problems.
However, a mutant elutes in the wash. After further purification with
size exclusion, I notice that this mutant is always associated with
some medium c
Dear all,
Now I'm solving a structure with 1.6A resolution. The data seems good with
R-sym (12.4) and all other parameters. Actually the data was collected with
SAD phasing. When we checked the data we couldn't find the Se atom in the
structure. Since the data resolution is good, we tried to do
Slightly off-topic - but these days most crystallographers are
interested in protein purification.
What experience do people have with silica based columns for size
exclusion chromatography. We are interested in resolution, stability,
column life time, and ease of cleaning column compared to
Dear All
the latest test version is on the ccp4 ftp server.
ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-core-src.tar.gz<- core ccp4,
rapper, clipper
ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-phaser-src.tar.gz <- cctbx and
phaser
ftp://ftp.ccp4.ac.uk/ccp4/6.1/ccp4-6.0.99e-balbes_db.tar.gz
Hi Kendall:
I haven't used CCP4Mg^2+ but if it is launched by a shell script that
dumbly sets the DISPLAY variable, then on 10.5 this is equivalent to a
suicide directive, since the new X11 (as of 10.5) sets the DISPLAY
variable using launchd. If this is the case, hack that line out of
t
Research associate position to work in the Membrane Protein
Laboratory, Oxfordshire
A post-doc position is available to work in the Imperial College
Membrane Protein Laboratory
(http://www.diamond.ac.uk/Science/MPL/default.htm) at the Diamond
Light Source Synchrotron,
Oxfordshire (http://
Good Day,
This is my first post on ccp4bb, and I am seeking advice on a problem I have
encountered.
My crystal structure revealed a nickel ion chelated by 4 nitrogen atoms: 3
from protein chain A and 1 from chain B. A and B form dimers. The nickel
was placed in the same asymmetric unit as chain
CCPMG is launching X11 right before it quits. Could it relate to the version
of X11? Coot was not working with the version that updates with the OSX, so
I had to install the Xquartz version to get Coot to work.
Kendall
On 7/25/08 10:53 AM, "Jendrek" <[EMAIL PROTECTED]> wrote:
> Hi,
>
> I've
In addition to Bert's statistics argument (I've never had the pleasure
of working w/ a C222 crystal), do check your self-Patterson map. I
recently had a difficult MR case; the crystal masqueraded as P21212 or
P2221, but it was actually P212121 with the two molecules in the AU
related by a non-cryst
Hi,
I've had the same problem and discovered that in order to start CCP4MG the X11
must be closed.
So, just quit your X11 and then start again. It worked fine for me.
Andrzej
Kendall Nettles wrote:
I have tried installing the newest version of CCP4MG 1.1.1, the closedirfix
version, and QtMG
I have tried installing the newest version of CCP4MG 1.1.1, the closedirfix
version, and QtMG 1.99.0. In each case, the program does not start. I did
get a problem report for pyton, shown below.
Mac ppc dual 2.7 GHz, OSX 10.5.4
X11= XQuartz 2.3.0(xorg-server 1.4.2-apple5)
Any suggestions would b
Hello all!
Does someone have experience in minimize energy instabilities in
beamlines?
MX2, our new beamline devoted to MX experiments, are facing problems
with energy drifts. As far as we could notice, theses drifts are results
of the contribution from several sources - possibly electron beam
m
Good point. One should always check all the screw axis combos. Not fun
for P422, but Phaser makes this very easy, as it will do all the
possible screw axis combinations in one job. The correct space group and
MR solution is usually very obvious if the model is acceptable and the
MR parameters h
Regarding Phil's comment about the space group, check the PBD stats and you'll
see that c222 is pretty rare. It occurs only in 0.24% of all cases, versus 5.1%
of C2221. So i guess you could say that without doing any analysis, there's a
95% chance that a centered orthorhombic cell is c2221 rathe
Perhaps obvious - are you sure the space group is C222 not C2221?
Phil
On 25 Jul 2008, at 14:19, Roger Rowlett wrote:
Carl Soja wrote:
Dear all
I tried to solve one structure by ccp4i molrep(resolution at 3.0 A,
space group C222, sequence ID 30%). I can get a good Rfactor 0.528
at first
Carl Soja wrote:
Dear all
I tried to solve one structure by ccp4i molrep(resolution at 3.0 A,
space group C222, sequence ID 30%). I can get a good Rfactor 0.528 at
first translation function. However, the second translation function
Rfac is 0.526, the third is 0.525, the fourth is 0.525.
Dear Debajyoti
Thank you very much for your help.
I input the each peak values as 10 and carried out the rotation and
translation function again.
I didn't get a improved solution by molrep.
can i edit the self-rotaion function and translation function solution file
as input ?
best regards,
carl s
If you are desparate, XPREP can apply symmetry transformations to
direction cosines (assuming that they are defined according to the
(1976) SHELX convention, i.e. relative to the crystal reciprocal
axes).
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen
Staff scientist position available at the EMBL-Grenoble
http://www-db.embl.de/jss/servlet/de.embl.bk.emblGroups.JobsPage/08054.html?EmblGR=x
We currently looking for a beamline scientist at the EMBL-Grenoble for the
mainentance, routine operation and further development of the highly successful
Dear,
I was wondering if it is possible to preserve the direction cosines
when converting an .mtz file (without scaling) to an .hkl file using
the CCP4 program 'convert'..?
(or perhaps another program..?)
Many thanks
Kristof
--
Kristof Van Hecke, PhD
B
Hi,
I dare to say about the possible way to do molrep from my recent experience.
You can choose "rotation and translation function" job at first and do the self
rotation fuction (for multimer) after that.Each of these run will generate two
different outputs *_rf.molrep_rf ans *_srf.molrep_rf
Dear all
I tried to solve one structure by ccp4i molrep(resolution at 3.0 A, space
group C222, sequence ID 30%). I can get a good Rfactor 0.528 at first
translation function. However, the second translation function Rfac is
0.526, the third is 0.525, the fourth is 0.525. All of the translation
34 matches
Mail list logo
