Hi Fred
Well, it is ironic that after acquiring ability to determine
a protein structure some times in a few minutes
we are still failed my format conversions like 30 years ago :-(
Dr Felix Frolow
Professor of Structural Biology and Biotechnology
Department of Molecular Microbiology
and Bio
I've a protein sequence of known domain. Based on structure
alignment,
I've got a alignment of those with known structures. Then how to add
my
sequence to the alignment?Any suggestions?
Hi Yuan,
You can use UCSF Chimera's Multalign Viewer tool to do this. Just
open your alignment with
Here is an incubator about the size of the Ecotherms but much cheaper:
http://www.tritechresearch.com/DT2-MP-38.html
We have one for insect cell culture that has worked great for several
years, and there is no vibration. However for crystallization we have
BOD incubators from Fisher.
Nat
On Mon
3-d coffee and expresso will align sequences without structures with sequences
that do have structures in a structure-based sequence alignment:
http://www.tcoffee.org/Projects_home_page/expresso_home_page.html
perhaps this is along the lines of what Yuan is looking for?
___
Does chainsaw not the opposite? Pruning a coordinate file based on
non-conserved residues identified in a MSA?
Yuan has a MSA of known structures and a sequence he wants to add to
it. I am always keen to learn about alignment programs, it would be
great to know how to use chainsaw for this problem.
http://en.wikipedia.org/wiki/SGI_Octane#Available_Operating_Systems
just googled "linux sgi o2"
On Tue, 2010-06-01 at 10:18 -0600, Brennan Bonnet wrote:
> Hi All,
>
>
>
> I just obtained a Silicon Graphics O2 Unix workstation from 1996. I
> want to use it for 3D modelling of protein crystals
Hi Brennan,
http://www.nekochan.net/wiki/index.php/SGI_O2
There is official Linux support for the O2 in Debian 4.0 "Etch" as
well as in Gentoo but only for R5000/R7000 O2s. Linux is not stable on
R1/R12000 CPUs due to a known issue with the way they handle
speculative loads and stores, detail
Hi All,
I just obtained a Silicon Graphics O2 Unix workstation from 1996. I want to use
it for 3D modelling of protein crystals using "Crystal Eyes Stereographics" and
I'm wondering if anybody knows of any versions of Linux which I could install
on it.
Thanks,
~Brennan~
Christian Engel wrote:
Dear All,
I am looking for a ccp4 program that reads in cif-files and converts
them into pdb-files, including the CRYST1 card. Can anybody suggest a
solution? I didn't find any in ccp4i, e.g. the coordinate utilities.
I also tried COOT to read in cif-files (downloaded
Tim Gruene wrote:
I would like to use "Rotate/Translate Zone" in coot for a single residue and
set the
centre of rotation at the nitrogen of the subsequent residue. Is there a way to
achieve this with Coot Version 0.6.1?
No [1].
Paul.
[1] Practically no, but actually, it might be. However
This would be a possible explanation, and certainly is a problem with
low resolution refinements, but the free R indicates that overfitting
is not the problem here. (I'm assuming that the proper choice of test
set has been made in this case.) In my experience, for very isomorphous
pairs of str
Dear all,
I would like to use "Rotate/Translate Zone" in coot for a single residue and
set the
centre of rotation at the nitrogen of the subsequent residue. Is there a why to
achieve this with Coot Version 0.6.1?
Cheers, Tim
P.S.: The "Torsion General" would be a good start, but it does not see
Hi Christian,
Had exactly the same problem (converting an mmCIF file into a PDB). I
located and installed CIFTr . The version I have running here is
ciftr-v2.053 . I am afraid I can't remember exactly where I downloaded
it from. I think it one of the PDB associated files.
Fred.
Christian E
http://sw-tools.pdb.org/apps/CIFTr/
On Tue, 2010-06-01 at 15:21 +0200, Christian Engel wrote:
> Dear All,
>
> I am looking for a ccp4 program that reads in cif-files and converts
> them into pdb-files, including the CRYST1 card. Can anybody suggest a
> solution? I didn't find any in ccp4i, e.g.
The rnase structure used as the $CEXAM for CCP4 is another example - a
typical coordinate set is 2sar.pdb
There one monomer binds the substrate very clearly, whilst the other is
blocked by crystal contacts.
Eleanor
ANDY DODDS wrote:
Hello,
I am solving a structure of an enzyme, which cryst
Dear All,
I am looking for a ccp4 program that reads in cif-files and converts them into
pdb-files, including the CRYST1 card. Can anybody suggest a solution? I didn't
find any in ccp4i, e.g. the coordinate utilities.
I also tried COOT to read in cif-files (downloaded from the pdb server). Fo
On Mon, May 31, 2010 at 9:15 PM, Dale Tronrud wrote:
> One of the great mysteries of refinement is that a model created using
> high resolution data will fit a low resolution data set much better than
> a model created only using the low resolution data. It appears that there
> are many types o
VERY, very common in the Pharma setting where we do hundreds of
ligand-bound structures on a given target. Other permutations of this
scenario, such as only one monomer's ligand displacing a ligand used for
co-crystallization when trying to exchange by soaking, etc. Zsolt and I
could share renin s
Hi,
It occurs quite frequently with renin for example, with two molecules in
the asu. Depending on the affinity and shape of the inhibitors both,
only one or neither of the sites may be occupied. The slight, but
significant conformational difference between the two
crystallographically independent
Hi Andy,
I'd say fairly common, and there can be several reasons. One is that the
entrance of the active site (in case of crystal soaks) is blocked in
some subunits. Also, different affinities in the different active sites,
plus allosteric effects, are possibilities to consider.
The latest e
Dear BBers
There is an ~18 month vacancy in my lab for a postdoc to work on
our favourite macromolecular complex, the 'stressosome'. The ideal
candidate will know their way around an Akta and be able to solve
crystal structures by isomorphous replacement and/or anomalous
scattering. Experience of
Hello,
I am solving a structure of an enzyme, which crystallises as a dimer.
We have pretty good evidence that this operates as a dimer in vitro,
also. We have an inhibitor of this enzyme, which we are keen to
visualise by X-ray methods.
We seem to have very strong density in which we can model o
BEAMLINE TECHNICIAN
European Molecular Biology Laboratory, Hamburg, Germany
A position is available at the Structural Biology Unit of the EMBL in
Hamburg. The Unit utilises synchrotron radiation at the German
Synchrotron Research Centre (DESY) for research in structural biology.
EMBL operates
chainsaw does just that
eleanor
商元 wrote:
Hello, everyone,
I've a protein sequence of known domain. Based on structure alignment,
I've got a alignment of those with known structures. Then how to add my
sequence to the alignment?Any suggestions?
Regards,
Yuan SHANG
You are in luck - it is the total CC over all grid points used for that
Table
Eleanor
Hailiang Zhang wrote:
Hi all:
Thanks for all kindly helps with real space CC. Now I have a new question
again. In the output of OVERLAPMAP in CCP4, there is a almost last line
saying "Total...":
#
Dear All,
A position has become available for a Research Associate in the
Membrane Protein Laboratory (MPL) for crystallisation,
crystallographic and biochemical studies on bacterial antibiotic
transporters. The successful candidate will work on improving the
crystals and solving the stru
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