Hi,
these are still shared libraries - just that they don't want to load
any other shared library. Have a look at
% file libccp4c.so libccp4c.a
% ldd libccp4c.so libccp4c.a
to compare static library (*.a) and shared one (*.so). You'll see the
difference. So everything is fine and as expected
Hello,
trying to compile CCP4 6.1.1 on a Solaris machine, I just came across two
scripting errors in install.sh:
1. The syntax used in manifest.sh is valid for bash, not for the boune shell
called in install.sh; should use SET and EXPORT commands sequentially.
2. After asking for path names, t
I wouldn't use any stock solution that has been sitting around for a year at
4C. Why take the risk that something has happened with it/grown in it? Use a
freshly made solution and do not store it at 4C.
Bert van den Berg
University of Massachusetts Medical School
Program in Molecular Medicine
Bi
hi folks
i've almost got my B-factors questions sorted out. one thing i still
don't understand is this:
in truncate's wilson plot, what is plotted on the vertical axis is not
ln I_mean, but ln (I_mean/ff_mean)
and ff_mean (or Mn_ff, as truncate calls it) is the "average expected
value of ff".
Dear all,
please note that the current XDS package binaries won't work after Mar
31, 2008.
Binaries which expire Dec 31, 2009 are now available from the XDS
website, http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/ . For a list of
changes please check out the Release Notes.
best wishes,
Ka
The original poster may be interested in this paper from Phil Bourne's
lab a few years ago which looked at the contribution of folds (among
other things) by the Protein Structure Initiative, particularly Fig 5
and table 1.
http://helix-web.stanford.edu/psb04/bourne.pdf
"The Status of Structural G
Concerning the number of proteins folds in existence vs. the number of
folds already identified:
Ed Berry had some good points regarding sample statistics, and I assume
the mathematics of that sort of thing is formalized somewhere. The
number of examples per protein fold will be skewed by the comm
Hi all,
There is a 10 residues loop in my structure which has two conformations, how
could I show the double conformations at the same time in ribbon or cartoon
model in PyMol?
Thanks!
yamei
We haven't tried SUMO, but had some frustrating results with
GST fusions. They did improve expression and solubility - BUT
in one case the target protein precipitated immediately when
the tag was cleaved off, and resisted all attempts to bring it
back to life. In another case, the fusion protein
Hi everybody,
I know this is not the coot discussion list but right now I have
technical problems with the Internet connection and I could not
subscribe it. Here comes my problem.
I just installed in a new computer the last distribution package of CCP4
with Coot included. After installation th
Like most things (and scientists in general I suppose), SUMO tags have both
a good and a naughty side. Like GST, in my hands, they enhanced expression
and solubility of a couple of different target proteins. Their primary
advantage is that when you clip off SUMO with the SUMO protease (aka Ulp1)
th
Some thoughts about SUMO tags and fusion tags in general.
Fusion tags also follow the "Garbage In, Garbage Out" philosophy.
Yes, if for many of the reasons already hashed out extensively on
CCP4BB, one is dealing with lack of expression or miniscule
expression, often tagging the protein wit
The School of Crystallography/Institute of Structural and Molecular
Biology is seeking a Post-doctoral Research Assistant to carry out
structural analysis (x-ray crystallography or cryo-electron
microscopy) of complexes formed during pilus biogenesis. The group is
led by Professor Gabriel W
Hi everybody!
I am using coot version 0.5.
I am trying to build a DNA sequence in my model.
At certain positions when i add residues and then used "simple mutate" to
make it according to real sequence, it always add ribonucleotide (guanine
ribonucleotide, Gr) in place of deoxyribonucleotide (guani
Matt Warkentin wrote:
> hi folks
>
> i've almost got my B-factors questions sorted out. one thing i still
> don't understand is this:
>
> in truncate's wilson plot, what is plotted on the vertical axis is not
> ln I_mean, but ln (I_mean/ff_mean)
>
> and ff_mean (or Mn_ff, as truncate calls it)
Although there are more elegant ways to do the same, an easy way is
to simply write out either just the loop region or the entire
molecule containing the second conformation into a second PDB file
and to simply read in the two PDB files as two separate molecules in
PyMol.
Raji
On Feb 26
Hi,
I respectfully disagree with the doom&gloom feelings regarding fusion
proteins. In my not very limited experience, fusion proteins *can* fix
expression issues. Do they always work - of course not :) But there are
very few things in this field that work most of the time. Is it better to
try a f
Concerning the contamination of recombinantly expressed proteins with
bacterial chaperones, one might wish to try a complete removal using ATP
and denatured protein as a "bait" as described here:
Protein Expr Purif. 2000 Oct;20(1):45-7.
Separation of copurifying GroEL from glutathione-S-tran
Hi,
is it possible that you installed for the wrong architecture, i.e., that
you have a 32bit machine/OS but picked a 64bit version? It's just a guess
(the interface uses tcl/tk so you would not notice from just starting the
GUI).
Tim
--
Tim Gruene
Institut fuer anorganische Chemie
Tammanns
Hi all,
I am trying to follow good practices and keep my set of free reflections
between data sets, eg. in this case between an in-house low resolution and a
synchrotron high resolution data set. High resolution data from hkl2000 were
imported through the ccp4i task, keeping the low resolution Free
Hi Yusuf,
I had a similar problem once when my pdb file did not have the right
format. Check your input coordinate file if your DNA nomenclature is
correct for coot. Maybe, the program does not recognize your molecule as
DNA.
Good luck,
christian
Yusuf Akhter wrote:
> Hi everybody!
> I am using
Thanks to Paul and Christian..for responding very quickly to my query.
I tried all versions of coot and it worked in only ver 0.4. Now everything
is fine.
Cheers!
Yusuf
On Thu, Feb 26, 2009 at 7:04 PM, Yusuf Akhter wrote:
> Hi everybody!
> I am using coot version 0.5.
> I am trying to build a
Dear all,
Thank you in advance for your expert opinions.
I am working on a peptidoglycan (PG)-binding protein, which is composed of
two functionally identical domains. Interestingly, when subjected to gel
filtration chromatography (Superdex 200), both full-length protein and the
single domains mi
Hello,
I wanted to know if there is a standard procedure for purification of
protein with ligand. I have never done this before so it will be nice to
get some help.
Thanks,
Mariah
--
Mariah Jones
Department of Biochemistry
University of Florida
Thanks a lot, Garib,
as always, there is a new version of refmac just out that fixes all the
problems.
Cheers
Jan
2009/2/26 Garib Murshudov
> I think we have fixed this problem just recently. The problem was related
> with refmac not being able to pick correct dataset from mtz. IF there was
> o
Dear Bart and Howard,
let's assume that the paper is novel. Without asking
too much, however, I think it would be fair to ask
why they used a homology model for molecular
replacement, when they claimed successful structure
solution two years ago.
Also, since they claim successful structure solut
Hi Mariah,
You may need to specify what type of ligand (is it a nucleotide, a
small synthetic molecule, a peptide etc ?) and also what is the affinity
between your ligand and your protein.
I have purified several protein-ligand complexes, you can go several routes.
If you have a high affinit
Hi,
I wouldn't call this a standard procedure - generally speaking the most
important two parameters you have to consider are: the protein/ligand
affinity and the supply of the ligand. For tightly bound ligands, you may be
able to just add the ligand once (i.e. during cell growth and expression
Look up a standard endotoxin assay (usually an immunoassay) because that's
exactly what endotoxin is :-)
Artem
---
When the Weasel comes to give New Year's greetings to the Chickens no good
intentions are in his mind.
_
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On
Dear scientists
I have asked a question in previous discussions regarding cryo conditions
for collecting data of a crystal. What is the cryo condition followed in a
small molecule data collection in olden days. I got wonderfull answers.i
am very happy for that. Is any one confused in this issue li
On Feb 25, 2009, at 11:45 AM, Jayashankar wrote:
But provided if i colud follow a pattern even blindfolded could come
up with some probable things.
Is it not ok to have principle of mathematical induction.
Or extrapolation. I would make a plot of new folds discovered by year
and extrapola
Hi,
Sorry for the off topic question. I am looking for helps from someone who is
familiar with Centramate from Pall. We recently bought one and try to use it
for concentrating insect media with secreted proteins. Here is some more
information:
Pump: MasterFlex Console drive
Pump head: quic
Hi all,
Once again I seem to have managed to kick up a minor debate on the
bulletin board (Note to self no more posts on SUMO or Apple :-[ ). With quite a few
years of experience working with SUMO I feel I can safely state that it
is a good enhancer of fusion protein production in E. coli
Apologies for the slightly frivolous language - technically peptidoglycan is
*an* endotoxin, as there's a separate entity also commonly referred to as
endotoxin which is the LPS/LOS component of the cell wall. Peptidoglycan is
also an endotoxin (or at least quite a few researchers consider it to be
Just a quick reminder, those of you who forgot about the "deadline"
for submitting some nice crystallography related pictures it will be
extended until March 9th.
I've received some really nice pictures and rendered images so far,
keep sending more.
2 per person, just as a reminder.
Jürgen
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