Dear Jochen and the others,
your problem is different from the one described here recently and a
different fix will be needed. One major difference is that in your case
CCP4 was installed via fink, while I have used the ccp4.ac.uk download
pages which as far as I can tell never resulted in an
Dear Bulletin Board,
Thank you very much for the information and comments. In the last days I have
learned a lot and it has been very helpful. It turned out that at the basis my
problems were the fact that sftools was not up to date and that I had been
looking in the wrong places for space
We are looking to fill (as soon as possible) a doctoral position in the
field of molecular enzymology and structural biolog at the Institute of
Molecular Biosciences of the University of Graz, Austria.
The studies aim at providing a detailed biochemical and structural
characterization of the
Dear bulletin board,
One postdoctoral position funded by the Academy of Finland is available in the
Antibiotic Biosynthetic Enzymes research group (ABE) at the University of
Turku, Finland. The position will be filled initially for one year, with a
possibility for extension for up to two
This is not really protein crystallography but we are trying to model build a
ligand into a protein binding site. A similar ligand is already in place and we
want to replace this by initially superimposing a phenyl ring which is common
to both ligands. We understand that such superpositioning
Fri. Sept 3rd 2010
EBI
Try ProFit
ttp://www.bioinf.org.uk/software/profit/
as you can give the atom names you want to fit.
Miri
On Fri, 3 Sep 2010, Rex Palmer wrote:
This is not really protein crystallography but we are trying to model build a
ligand into a protein binding site. A
On 03/09/10 12:44, Rex Palmer wrote:
This is not really protein crystallography but we are trying to model
build a ligand into a protein binding site. A similar ligand is
already in place and we want to replace this by initially
superimposing a phenyl ring which is common to both ligands. We
Dear Rex,
if you need to fit only one ligand, and if this fit is the starting
point for further model building, the quickest way to do it is to do a
manual superposition. (calculate - model/fit/refine/ - rotate/translate
zone). If you click twice on an atom of the phenyl ring, your ligand
will
Dear Rex,
You can try SPDB viewer if it serves your purpose.
Gauri
Dear all,
Giuseppe Zaccai showed me an interesting article about science funding
(from F.T.). I thought it could be of interest to all of us since we
have to apply for funding, and succeeding in securing funds is getting
more difficult all the time.
The scan of the article can be found on:
Dear Rex,
if I understood corrctly what you are looking for you could also use Gerard
Kleywegt's lsqman, where you can pick the atoms which you want to use for
superpositioning.
Tim
On Fri, Sep 03, 2010 at 12:44:03PM +0100, Rex Palmer wrote:
This is not really protein crystallography but we
Dear CCPeers
I wanted to thank everyone for sharing their experiences and giving valuable
advice on CYP51 protein expression. It seems that special vectors like pCW-Lic
or pcWORi is needed for efficient expression. I have not found any commercial
source for them though. Could anybody be
Dear All,
I am encountering a problem when using Parrot (for combined density
modification and non crystallographic symmetry (NCS) averaging) in
ccp4 6.1.13, run via ccp4i.
Parrot does not detect the (2-fold) NCS present among my heavy atom
substructure with 20 seleniums (the pdb was
Hi Rex,
the command
phenix.superpose_ligands 1.pdb 2.pdb
will do it.
1.pdb and 2.pdb are two PDB files containing the ligands. The output
result will be in overlay_1_pdb_2_pdb.pdb file. The algorithm is based
on graph matching, and it is good for ligand-sized molecules. The atom
labels
Dear BB,
I'm stuck with PVM (Parallel Virtual Machine) right now, trying to tell the
master to use a remote host as slave.
The individual machines run fine with PVM but they don't seem to communicate
with each other and I don't even get an error message, which makes it hard to
troubleshoot.
Dear All,
It is a Pymol question. How can I set up the view through one axis of the
unit cell?
Thanks a lot and have a nice weekend,
Jerry
On Sep 3, 2010, at 4:03 PM, Jerry McCully wrote:
It is a Pymol question. How can I set up the view through one
axis of the unit cell?
By eye. Use orthoscopic view to help. Show the unit cell as a guide:
http://www.pymolwiki.org/index.php/Cell
James
Hi Jin,
Could it be the wrong amino acid in the sequence? Have you sequenced the gene
construct that you used? The codon usage for HIS is CAC or CAU, and for TYR is
UAC or UAU. -
Cheers, Janet
From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On
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