It is recorded by SCALA - if you use that data processing procedure.
You can still do a run of scala after SCALEPACK or XDS or whatever
providing you output integrated, unmerged intensities.
You are right though - we need a data analysias tool..
Eleanor
James Pauff wrote:
Hello all,
Silly
Hi Adam,
The symbolic link approach does not work - I hit this problem with
another (C++) program. Your pointer about the compat rpm is helpful
though - this is probably the most robust solution. I ended up compiling
from scratch when I hit a similar problem.
Best,
Graeme
-Original Message
Dear all,
We have installed CCP4 6.0.2 in Fedora core 8. While running the program we
are getting the following error message-
error while loading shared lilbraries libstdc++.so.5, cannot open shared
object file: no such file or directory.
Please suggest how to get this library file...
Thanx in ad
Dear Shivesh,
I believe that Fedora 8 has a more updated version of
libstdc++ in /usr/lib. You can install libstdc++.so.5 from
compat-libstdc++-33-3.2.3-62 using yum (if you have it). An
easier approach would be to make a symbolic link between
libstdc++.so.5 and libstdc++.so.6 but there maybe
Dear all,
Sorry for the off-topic question...
What can be done to avoid a protein going inside inclusion body.The gene is
cloned in pET30a with C-ter his tag and expressed in BL21-DE3 from 37 to
18C for 3-4 hr with .5mM of IPTG,it is going to inclusion body.All
suggestions are welcome.
Thanx in ad
Dear all,
Sorry this might be another naive, non-ccp4 question~
I was trying to make a composite omit map with CNS, but during torsion angle
dynamics, it always reports an "argument out of range" error like the
following:
-- step= 5 at 0.02000 ps
Lower temperature, use chaperones (e.g. TAKARA set), refolding?
Quoting shivesh kumar <[EMAIL PROTECTED]>:
Dear all,
Sorry for the off-topic question...
What can be done to avoid a protein going inside inclusion body.The gene is
cloned in pET30a with C-ter his tag and expressed in BL21-DE3 fr
I am looking for software or a server to run the 3D-1D profile search
in reverse: that is I have a new structure (not in yet deposited in
PDB) and I want to see what sequences might fit well to this 3D
structure.
Can someone point me in the right direction?
-jason
Hi Jason,
While it's not quite what you described, I'd recommend you check out the
Secondary Structure Matching server at the EBI:
http://www.ebi.ac.uk/msd-srv/ssm/ssmstart.html
That will (hopefully!) give you previously deposited structures which share a
similar fold to your query pdb file.
Also worth trying a lower IPTG level ~ 0.1mM and or different media,
e.g. TB, SOC or m9 instead of LB, it's all a bit random but sometimes
these things can make a difference. Adding 3% EtOH on induction
worked for me once, it's supposed to shock the cells and stimulate
chaperone production
Dear All,
Anyone have experience with the NovaGen Duet co-expression vectors? Or
can recommend others?
http://www.emdbiosciences.com/html/NVG/Duet_Spot.html
Greetings,
Mark
Mark J. van Raaij
Dpto de Bioquímica, Facultad de Farmacia
Universidad de Santiago
15782 Santiago de Compostela
Spain
Dear Skivesh,
My favourite media is TPB - (paper is: Moore et al Protein expression
and purification (1993) 4: 160-163). I've had luck with this and
BL21 (DE3) Gold cells. I'm also a fan of cold shocking cells - after
initial growth at 37 deg C, put flasks in an ice water bath for 10
min, th
I do use the Duet vectors extensively and they work just fine. I have trouble
with my protein
complex, but that is solely related to my proteins. My lab mate has used these
vectors very
successfully.
I have been using pRSF-Duet and pETDuet1 more than pCDFDuet1 or pACYCDuet1 for
no specific rea
Hi all,
The data I am working on has a strong translation vector. The space group
is C2221 and resolution is 2.3 angstrom. There are two molecules per AU
with a pseudo-2-fold axis.
On the cumulative intensity distribution plot, the theor and obser curves
totally do not overlap. I did "detect_twinn
Dear CCP4 Members,
Apologise for a non-ccp4 question.
Could anybody give the difference between "blue confocal max-flux optics"
(supplied by Rigaku) and "osmic confocal max-flux optics" (supplied by ?).
Are they use same technology (i.e. max-flux) or different?
Thanking you
Sincerely
Karthik
Hi Qiang,
A normal data set has a unimodal intensity distribution with a
predictable shape. When there is twinning the distribution remains
unimodal but becomes sharper and this is picked up in the twinning
analysis. When there is pseudo-translational symmetry, as you indicate
you have, then
Hi Jason,
RosettaDesign server will do just that:
http://rosettadesign.med.unc.edu/
You can specify that certain residues remain unchanged (say active site),
that they fall into defined physico-chemical categories (polar, hyrophobic,
etc), or let the server change all residues into whatever i
Hi,
If you are expressing just two proteins, you could try a single pET vector with
a pCDF vector. The only reason I'm suggesting this is that I had trouble with
pET-Duet, but doing each one separately worked first time (plasmid size
issue?). I used pET24-a and pCDF-1b - so I had one construct
We have had good experience with the awfully simple minded approach
of using two pET vectors with different antibiotic resistance.
Its the easiest thing to do, and it often works ...
Apologies for the shameless plugin, since there are many good papers
on the subject, but you can read some hin
I thought only I was having trouble with cloning into pETDuet1. But just to add
to what someone just
said Yes, I had hell with trying to get one of my ~2kb fragments into
pETDuet1 (5.4kb). Could be
a combination of vector size and insert size.. Who knows!
Sometimes, I do what Tasos says: Tra
Just to explain to people who've never had to do co-expression - if I remember
correctly, conventional wisdom states that you can't have two different vectors
with the same origin of replication in the same host (maybe someone might know
more details as to why). However, as pointed out, it can
Hi Mark,
Proper co-expression in trans requires that you use plasmids each with
different origins of replication and antibiotic markers, such as p15 +
Kan and ColE1 + Amp. I think the pET vectors of the DUET system use
these two origins (p15 and ColE1). This ensures much more efficient
Dear all,
Anyone know about how to transfer a 3D image (ligand + protein surface) into
a format that would be compatible for 3D laser engraving in plexiglass.
I am aware of a few cies that can provide the final product (see below) but
we are looking for file format information
Luminorum (UK)
Cr
Howdie folks:
I've got what appears to be an inner-sphere interaction between Mg++
and the N7 of a G. The mode of binding is the same as what is observed
at this site for Mn++, confirmed with anomalous data. Our resolution
is 1.6 Å, so I am reasonably confident this is right. However, my
Sorry, I should have been less cryptic:
On Apr 2, 2008, at 2:13 PM, Jacob Keller wrote:
Forgive the naive questions:
To what do the terms "hard" and "soft" refer here?
In inorganic chemistry, "hard" refers to bonding where the Coulomb
potential dominates, and "soft" where orbital terms do
Dear Rene
I have used a company called Imaage in Australia for engraving
proteins in glass blocks. Their web address is
http://www.imaage.com.au/
I send them VRML output from MOLSCRIPT and that usually works fine.
You need to generate the image in a single color (black), though you
can u
Dear all,
Dose anyone have experience about the production of recombinant membrane
protein complex in E. coli? All suggestions are welcome.
Thanks in advance.
Yi-Wei Chang
Institute of Molecular Biology
Academia Sinica, Taiwan
Hi Bill,
On Apr 2, 2008, at 10:58 PM, William G. Scott wrote:
I've got what appears to be an inner-sphere interaction between Mg++
and the N7 of a G. The mode of binding is the same as what is
observed at this site for Mn++, confirmed with anomalous data. Our
resolution is 1.6 Å, so I am
William,
it is not clear from your message why you think this is a Mg++, not Mn++
which has been observed in this site before? Mn++ would be visible in
anomalous data from a home source, but not Mg++. The only way to
distinguish Mg++ and water is the number of coordination which should be
very
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