Dear BBusers,
Could you point me to a few classic reviews on enzyme engineering? In
particular:
a) pH, thermal pressure stability
b) de novo design
c) increasing low temperature activity
Regards,
Partha
Dear All,
I decided to use a LIC vector with enterokinase cleavage site for His tag
removal. Of course I did not check the length of the linker (about 45 aa) nor
if the enterokinase cleavage site would be the best choice
Do you know where I could purchase a decent quality with
Dear all,
I have successfully compiled ccp4 6.2.0 on an OSX (10.6.8) machine but
I'm failing to do the same in a different one, though with the same
system setup. In the machine giving me trouble I want to install ccp4 in
a nfs disk mounted. When I run configure using exactly the same input as
in
Dear Miguel,
yes, I hit the same issue - and for me the machine then completely
freezes and needs a reboot.
The patch for configure:
--- configure.orig 2011-05-05 16:07:55.0 +0100
+++ configure 2011-07-21 16:05:57.0 +0100
@@ -3206,6 +3206,9 @@
if test $system =
When I've built CCP4 on OSX I've just used configure with no arguments it's
worked
On 2 Aug 2011, at 12:59, Miguel Ortiz Lombardía wrote:
Dear all,
I have successfully compiled ccp4 6.2.0 on an OSX (10.6.8) machine but
I'm failing to do the same in a different one, though with the same
Dear list,
On Tue, 2011-08-02 at 13:03 +0100, Clemens Vonrhein wrote:
Dear Miguel,
yes, I hit the same issue - and for me the machine then completely
freezes and needs a reboot.
I wrote this mmap test (back when VMS was still supported by CCP4, and
porting CCP4 to Mac's was just an idea
Dear all,
A question for PYMOL. The command print cmd.align will align two pdbs and
print out some informations like:
(3.7496898174285889, 42, 1, 3.7496898174285889, 42, 20.0, 2)
My question is what are the meaning of those number? which one is RMSD?
Many thanks!
G
The numbers are:
1) RMSD after refinement
2) Number of aligned atoms after refinement
3) Number of refinement cycles
4) RMSD before refinement (raw sequence alignment)
5) Number of aligned atoms before refinement
6) Raw alignment score
7) Number of residues aligned
The refinement drops
On Tuesday, 02 August 2011, Peter Keller wrote:
Dear list,
On Tue, 2011-08-02 at 13:03 +0100, Clemens Vonrhein wrote:
Dear Miguel,
yes, I hit the same issue - and for me the machine then completely
freezes and needs a reboot.
I wrote this mmap test (back when VMS was still
Dear ALL;
We are going to use the prescission protease cutting site (LEVLFQ/GP
) in our cloning vector to remove the His6 tag.
Do we need to insert some linkers between this cutting site and the
target protein to improve the cleavage efficiency?
Or we are
Dear McCully,
I always used this protease with a cleavage success near to 100% at 4°C over
night without shaking.
Concerning the construct, I putted the first Met just after the sequence
LEVLFQ/GP SSP, so I added only three aminoacids after the cleavage site.
All the best,
Marco
Il
Dear Colleagues,
We are pleased to announce the EMBO|EMBL Symposium:
Structure and Dynamics of Protein Networks, 13 - 16 October 2011
Please visit the conference website: http://www.embo-embl-symposia.org.
The symposium will take place in Heidelberg, Germany at the EMBL Advanced
Training
I can launch the program after installing the newest package from
the Website
Thank you all,
yuri
On Mon, 1 Aug 2011 17:01:47 +,
ronan.kee...@stfc.ac.uk wrote:
Dear Yuri,
Are you still
encountering problems with this? I've made the changes to the CCP4
download site so that the
Dear CCP4 experts,
I would like to ask if there is a clear way to distinguish Na+ and HOH
molecules in the electron density map. The table I have suggests Na
to O distance lies between 2.35 and 2.45 that is very hard to discern
the difference of these two candidates. Na+ may have several
I asked the CCP4 experts this question a while back--maybe try
searching the archive? There were some very helpful comments.
Jacob
On Tue, Aug 2, 2011 at 1:24 PM, Young-Jin Cho yj...@brandeis.edu wrote:
Dear CCP4 experts,
I would like to ask if there is a clear way to distinguish Na+ and HOH
Dear Young-Jin,
If you model it as water, you can use WASP. It's an old program but still
accesible here: http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl
Cheers,
Robbie
Date: Tue, 2 Aug 2011 14:24:09 -0400
From: yj...@brandeis.edu
Subject:
Hi Robbie and all-
The link from that page is dead...and an inquiry to the webmaster bounced.
Anyone know where WASP is now?
Thanks
Christina
Oklahoma State University
From: Robbie Joosten robbie_joos...@hotmail.com
To: CCP4BB@JISCMAIL.AC.UK
Sent: Tuesday,
Hi Christina,
The WASP server seems to working at this location (about half way down the
page):
http://www.jcsg.org/prod/scripts/validation/sv2.cgi
I hope that helps.
Take Care,
Sean
P212121
http://store.p212121.com/
Can anyone recommend a good fee-for-service facility that does routine high-res
mass spec on small molecules?
Probably best to reply off-line; and I'd ask you to limit suggestions to
facilities within the continental US (for reasons of convenience, rather than
chauvinism).
Thanks,
Pat
Hi,
I decided to give the server a try...and the output is:
FILE NOT FOUND:
/prod/tmp/individual_validation/output_wasp/25854/bindividual6Na.ion
Either my pdb does not have any metal ions or this server is currently not
working.
Sujata
On Tue, Aug 2, 2011 at 5:04 PM, Sean Seaver
Dear Jerry,
Our in-house series of vectors encode the Rhinovirus 3C-protease site, followed
directly by a NdeI site, which after cleavage leaves just GPHM on the front of
your protein. We routinely get 100% cleavage with incubation overnight at 4˚C
— and have several xtal structures to boot.
Hi Jacob,
Darn that site doesn't seem to be working. I generated the files ion files and
thought it was good to go, but didn't view the outputs.
Apologies,
Sean Seaver
P212121
http://store.p212121.com/
Search for Metal Cordination sites in Proteins.
It takes you to a site set up by Marjorie Harding which gives a table of
known metal coordination extracted from the PDB including Na.
Of course there may be errors in the PDB entries but it is very helpful I
find
Eleanorr
On Tue, 2 Aug 2011
23 matches
Mail list logo
