Dear All,
I wanted to solve one of my new structures by molecular
replacement. I got three short search motifs from three
different structures available in the PDB. My question is, how
do I use all the search models to solve the structure.
With by best regards,
Sekar
(\_/)
(='.'=)
(
should i take it that when given > 1 .pdb in an ensemble, phaser will
output only the first member of the ensemble, and its up to the user to
tranform the others?
if so, i gather there are no keywords to make phaser do that
automatically?
-bryan
Xiaoyi,
When I'm interested in dimer interfaces, or protein ligand contacts I
usually use Molprobity to define the interface.
http://molprobity.biochem.duke.edu/
It is a bit of a process, but here's the rundown:
Load your .pdb into molprobity
Add hydrogens
Visualize interface contacts
Then sele
If you just want the residues involved in the interface, you can use the
byres selection commands in Pymol.
select contacts, (byres monA and (monB around 4))
which will show all the residues on monA that are within 4 Ang. of Mon
B.
Steve
-Original Message-
From: CCP4 bulletin board [
Hi,
apart from the ccp4 "contact" it's also worth checking the following
servers:
pisa:
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
protein-protein interaction server:
http://www.biochem.ucl.ac.uk/bsm/PP/server/index.html
Cheers
Nikos
Xiaoyi Deng wrote:
> Dear all:
>
> I used moleman2
You'd need quite a large French press or meat grinder to crack the cells
and get the protein.
William Scott wrote:
On Thu, 20 Sep 2007 17:23:05 +0100
"R. J. Lewis" <[EMAIL PROTECTED]> wrote:
a large signalling complex called the 'stressosome' from B. subtilis.
Dear all:
I used moleman2 to calculate the contacts between chain A and B. Can
anyone suggest a program to calculate the contacts between the interface
of dimer-dimer?
Thank you,
Xiaoyi
Graduate student
University of Nebraska Medical center
On Thu, 20 Sep 2007 17:23:05 +0100
"R. J. Lewis" <[EMAIL PROTECTED]> wrote:
a large signalling complex called the 'stressosome' from B. subtilis.
-
If you decide to go for the human form of this signalling complex, I am an
over-producing strain.
Dear all
There is a vacancy in my lab for a biochemist. It's a 3-year position funded
by the UK BBSRC. The post is to provide a functional interpretation of
our structure determination (unpublished) of a large signalling complex
called the 'stressosome' from B. subtilis. Ideally, I'm looking for
Go to the jiscmail page and follow the directions.
On Thu, 20 Sep 2007 16:31:07 +0200
Anat Bashan <[EMAIL PROTECTED]> wrote:
unsubscibe
unsubscibe
Dear Eleanor,
no I was not talking about a cubic SG (in my case, as an example, it's actually
orthorhombic).
I think that the most likely explanation is that there was indeed a bug, at
least on Refmac's version 5.3.0032
Here go some selected fragments of a 0032 log (no confusion with aniso atom
Hi I think there you're confusing overall aniso scaling of the Fcalc's to the
Fobs's (normally the default) which is controlled by SCALE LSSC ANISO, and
refinement of individual atomic displacement parameters controlled by REFI BREF
ISOT/ANISO. In the script aniso scaling is turned on (even tho
On Sep 18 2007, Bryan W. Lepore wrote:
i wrote
"(ensemble) / (sequence)" to get a percent composition
i forgot to emphasize that i do not mean the Vm or the "Z" composition,
but the composition as one would enter e.g.
COMPosition ENSEmble mol1 FRACtional 0.22
or
COMPosition SCAttering
-b
I cant answer - but this version certainly generates anisotropic scales..
We have ccp4.6.0.2 installed)
###
###
##
I can't say because I didn't install 0037 (I went straight from 5.2.0019 to
5.3.0040 so I was blissfully unaware of the problem!). However according to
the original posting it's easy to tell because if the alleged bug is present
you don't see the overall Bij terms in the output PDB file.
HTH
16 matches
Mail list logo
