A postdoctoral position is available in the laboratory of Bert van den Berg at
UMass Medical School, Worcester (MA), to work on a NIH-funded project
investigating the mechanism by which hydrophobic molecules, such as toxic
xenobiotics, cross the bacterial outer membrane. The focus of the
Hi Ian,
A bug was reported with that version of Refmac, though I've no idea
if that would cause your problem: you should upgrade to the latest
version from the York website.
Done - and here is what happens:
1) the latest CCP4 package (6.1.1) runs the same version of Refmac
(5.5.0066)
Yes - I found that irritating bug; it is a disaster for less experienced
users..
It doesnt seem to happen with the linux installation..
Eleanor
Anita Lewit-Bentley wrote:
Hi Ian,
A bug was reported with that version of Refmac, though I've no idea
if that would cause your problem: you
Child killing and/or wrong bus seems to be related with static
compilation on Mac intel OS 10.5. Existence of this bug is the reason
why the version with bug fixes was not announced.
If you build from source code then this bug can be overcomed
Download source files and copy them to ccp4
Hi Folks,
If anyone wants to do this on an Intel mac you will need a fortran
compiler, which is not installed by XCode. There is a compatible
gfortran here:
http://r.research.att.com/tools/
which in my experience works fine, though is completely incapable of
producing static binaries.
There
I thought I'd post this to the CCP4bb, as judging by previous posts, it
seems I could get some useful insight into my problem...
This is question has probably been asked by people for a long as molecular
biology has been around, but hopefully my question isn't a complete rehash
of other peoples:
Hi,
The question you have to ask yourself first is - does my gene actually
*have* the rare codons that you're trying to avoid? Experience shows that
usually it's not single codons that are a problem but pairs or triplets of
rare ones. If your gene does not have obviously bad codon combinations
Thanks for the reply.
I've checked my sequence for rare codons; however, what would be useful to a
pseudo-molecular biologist like me is a web server which will look at your
input DNA sequence and guesstimate the success of expression in E. coli
(i.e., consider codon frequency). Does one exist?
Just to add couple of things to what Artem said..
If it is something similar to a mammalian kinase or malaria protein for
example,
1. Recodonizaton can change expression from near zero to substantial
amounts, however,
a) ideally, it needs to be recodonized separately for each target expression
This website is quite useful (via Expasy):
http://gcua.schoedl.de/
Raphael
Mo Wong schrieb:
Thanks for the reply.
I've checked my sequence for rare codons; however, what would be
useful to a pseudo-molecular biologist like me is a web server which
will look at your input DNA sequence and
Hi Mo,
Gene synthesis is definitely something you should try if you can afford
it.
However, I would suggest also trying to change expression plasmid and in
particular induction system and promoter system.
For toxic proteins we had some success using the pBAD (invitrogen)
expression system using
Dear all,
I am running SCALA using ccp4i. The generated command file is:
Hi James,
You are the victim of an epic command line. This has been fixed in the
6.1.1 release, but you will find that using a shorter path (i.e.
noniso rather than non-isomorphism c.) will pull the command line
down to something more sensible.
CCP4i writes this out to allow the job to be rerun
Hi,
Servers to check for rare codons definitely do exist.
http://genomes.urv.es/OPTIMIZER/
http://www.doe-mbi.ucla.edu/~sumchan/caltor.html
and several others
As to comparing Rosetta and Codon+ - your best bet here is just to dig up
product literature from the manufacturers.
Rosetta uses
Mo,
Just to add my 50 cents, I didn't see any mention of the use of
fusion proteins in your original post. GST, MBP or my personal, and
completely biased, favourite SUMO (plus many more proteins) have been
shown to enhance expression when fused to the amino terminus of a target
protein. If
hi
i am working on crystallisation of a 42 kDa his tag protein but,my protein gets
precipitated at higher concenrtration till now i have not tried any salt to
stabilise the protein,i am just confused what to do???should i go for higher
salt concentration or anything alse.
-Original
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