this bug was introduced in November 2008 and
fixed in February 2009
please use latest version from my home page
http://www.ysbl.york.ac.uk/~alexei/
Alexei
On 31 Mar 2009, at 20:10, Francis E Reyes wrote:
Why do i keep getting an error when running molrep with locked
rotation functions?
Op
Liew Chong Wai wrote:
Hi,
Good day
I am currently building my structure by using COOT. My protein is a
tetramer protein and I have fit my protein sequence into one of the
monomer of the homologous model. May I know how can I replace
other monomer with the amended monomer??
Thanks
*Chong-w
Dear All:
Hi. I have a question about selecting weighing term during restrained
refinement using Refmac5 of CCP4 packages.
For a 300kDa homodimer protein structure at 2.5A, 91% complete. I obtain
optimal R and Rfree by using NCS tight restraints of the peptides of the
Hi,
Good day
I am currently building my structure by using COOT. My protein is a tetramer
protein and I have fit my protein sequence into one of the monomer of the
homologous model. May I know how can I replace other monomer with the amended
monomer??
Thanks
Chong-wai
Around here, I would guesstimate the success rate to be in the
5-10% range. Still, I always try it as it's so easy. I don't think
longer soak times will usually do much to increase occupancy. Instead,
try higher halide concentrations.
I also like to try monovalent cations (Rb, Cs) but h
Hi,
Since a surprisingly large number of people asked for the protocol, I
compiled a quickie PDF document and posted it here:
http://www.xtals.org/pdfs/iodination.pdf
Please excuse the inevitable consequences of haste - I am sure that the file
is riddled with spelling errors and poor grammar. On
Greetings All --
I am posting this on behalf of the HR department here at Exelixis. Our
Fermentation department provides all of our protein resources for
high-throughput assay, cell biology and structural biology. Our structural
biology protein "consumption rates" are comparable to the large
The conditions in the drop play a huge role in the success of iodination.
If you see iodinated histidines, this means that you had high pH - higher
than 8 at least, as histidines are much harder to iodinate than tyrosines
(which will work even at pH 5, and definitely at 6).
Paul's classic experime
Hi everyone,
the in situ iodination reaction described in the following classic paper by
the late Paul Sigler works quite well.
Iodination of a single tyrosine in crystals of alpha-chymotrypsin.
Sigler PB.
Biochemistry. 1970 Sep 1;9(18):3609-17.
The primary purpose of my experiment (which took pl
Somewhat to our surprise, we have found that, even when the halide
signal is too weak to solve the substructure from scratch, when you
find the sites (in our case, by using the protein model as a
"substructure" in Phaser), they can still add significant phase
information. So you can get mo
I was wondering if anyone has used regular IPTG (not IPTG-dioxane free,
special
grade) for protein expression.
Are there any problems using such regular samples (5mg dioxane per Kg of IPTG)
for protein expression?
I have. No problem whatsoever. I belive the whole dioxane-free thing is
about
Hi,
it worked very nice for me in 1 out of 1 case where I tried it :-).
Very well diffracting crystals (1.8 Ang), rather small protein 20
kDa, 50 %solvent content, 1 mol/ASU. 20-30 s soak in 0.5 M NaBr
resulted in 6 nice ordered sites.
It was crucial for us to collect a 3 wavelength MAD da
Why do i keep getting an error when running molrep with locked
rotation functions?
Open failed: Unit: 8, File: /tmp/francisreyes/
qv_9_molrep_crossrot_alo.dat (logical: /tmp/francisreyes/
qv_9_molrep_crossrot_alo.dat)
MOLREP(ccp4): Open failed: File: /tmp/francisreyes/
qv_9_molrep_crossr
Dear CCP4bb users,
I was wondering if anyone has used regular IPTG (not IPTG-dioxane free, special
grade) for protein expression.
Are there any problems using such regular samples (5mg dioxane per Kg of IPTG)
for protein expression?
It would be great to have an idea for real problems if using thi
Would you put the iodide protocol on the wiki? If not, please send it to me
directly.
JPK
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
Dallos Laboratory
F. Searle 1-240
2240 Campus Drive
Evanston IL 60208
lab: 847.49
I'd like to remind folks here that if one's crystals are sturdy enough to
survive halide soaking, they're *probably* also sturdy enough to live
through covalent iodination. Iodination is easy to set up and if it does
work out - one gets awesome quality derivatives with multiple sites (as
long as th
You always get the entry of Bromide into crystal by quick soaking,
because it does not require the incorporation of Bromide into the
protein. But whether the signal is good enough for phasing is another
story. You have to collect the full data set to know the answer.
Nian
2009/3/31 tat cheung che
We were on a Br-soak flurry for awhile, and when I also talked to others,
it would work about 20-30% of the time. A few years I compared a structure
with Se-Met and native with Br-soak. There were four Br's at about 30%
occupancy, and it phased fine. It wasn't as good as the Se-Met phasing,
but we
On Tuesday 31 March 2009 09:57:13 Jose Antonio Cuesta-Seijo wrote:
> Hi!
>
> Normally the cell parameters, etc change very very little. You'll
> only know if the bromides got in at the synchrotron by looking at the
> fluorescence spectrum
That won't help, normally. It only tells you that th
Hi!
Normally the cell parameters, etc change very very little. You'll
only know if the bromides got in at the synchrotron by looking at the
fluorescence spectrum and at the anomalous signal. Normally some will
make it in and some will be in ordered sites, then it becomes mostly
a question
Hi all
I am now trying to do bromide soaking, but i am not really sure does the
bromide atom enter my crystal. So is there any signs that indicate the entry of
bromide atom? e.g. does the space group, cell dimension change? or just nothing
change, and the bromide atom just get in?
Thanks very
You can transfer the omit map from cns format to ccp4 or o map using
mapman . Then you can load and show it in pymol.
Good luck!
liu
xu zhen wrote:
Hi,everyone,
I want to present the ommit density map on my structure, It will be
great if someone can suggest the software and a brief instructi
Hi,everyone,
I want to present the ommit density map on my structure, It will be great if
someone can suggest the software and a brief instruction on how to use it.
_
More than messages–check out the rest of the Windows Live™.
h
Hi Hari,
Right terminal residues for constructs.
some time back there was some discussion with this subject.
you can check that threads also.
S.Jayashankar
Research Student
Institute for Biophysical Chemistry
Hannover Medical School
Germany.
On Tue, Mar 31, 2009 at 5:10 AM, Ho-Leung Ng wrote:
Ii is commented out in mine as well. But even deleting the # does not help
In fact this is the full log from configuration:
.
.
.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets
Associate Director Protein Expression Group, Novartis Institutes for
Biomedical Research, Basel, Switzerland
Job description:
As Group Leader in the Structural Biology Platform (SBP) within the Center
for Proteomic Chemistry you will lead a group dedicated to all aspects of
protein expression i
> Dear All,
>
> I wonder how people currently do their long term backups. I see
DATs/DLTs being slowly dropped off at the beamlines and most people
brings their data home in external HDs.
>
> Anyone using blue-ray or double layer DVDs for long term backups? If
so what kind of hardware? Do you
I am trying compile Pointless from source as this is the only CCP4 bit which
hasn't compiled on my x86_64 machine (linux Ubuntu 8).
I cd into src/pointless and then try to run "configure.sh". This stops at a
point where it complains that it can't find ccp4_errno.h. That seems
odd, as I have decla
I agree absolutely with James - be as succinct as you like in a table
but include the verbose definition for each entry in the log file - or
at the very least in the manual. It should be easy to search for with
the table tag.
People will not go and read a reference..
Eleanor
James Holton wrot
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