It works again now. Sorry for the inconvenience.
--Gerard
On Tue, 9 Jun 2015, Xiao Lei wrote:
Hi All,
I am trying to get electron density map of some pdb structures, I know
there is a database called "Electron density server" (EDS
http://eds.bmc.uu.se/eds). But somehow these days I can not c
Hi Xiao,
I've written a bash script that does just you want.
Find it here -->
https://github.com/donaldraymond/crystallography-scripts/blob/master/PDB_data.sh
Run the script with a PDB ID. Like this "PDB_data 1yks"
The script downloads the PDB and sf.mmCIF files from the PDB. It then converts
Hi Xiao, you can also download from pdb_redo
http://www.cmbi.ru.nl/pdb_redo/ if a rerefined, updated and optimized
X-ray structure model is also ok for you. Depends what your intentions are.
Best regards, Georg.
On 06/09/2015 11:02 PM, Pavel Afonine wrote:
Hi Xiao,
just calculate it yourself
In addition to the other excellent suggestions you have received, you
can download the map for a re-refined version of a PDB entry at
PDB-Redo. The latest Coot has a button for that.
It appears that the EDS is down. I'll notify the authorities.
Dale Tronrud
On 6/9/2015 1:11 PM, Xiao Lei
Hi Xiao,
just calculate it yourself. All you need to do this are model and
reflection data files (and, desirably, free-r flags). For example, in
Phenix this is
phenix.maps model.pdb data.xxx
where xxx can be .sca, .cif, .cns, .hkl or .mtz or any mixture.
Pavel
On Tue, Jun 9, 2015 at 11:11 PM, X
Dear Xiao,
if the structure was published after 2007, you can download the data from the
PDB, too, and run structure and data through refmac5. You can use 'rigid body
refinement' to avoid distortion of the model.
Regards,
Tim
On Tue, Jun 09, 2015 at 01:11:58PM -0700, Xiao Lei wrote:
> Hi All,
>
Hi All,
I am trying to get electron density map of some pdb structures, I know
there is a database called "Electron density server" (EDS
http://eds.bmc.uu.se/eds). But somehow these days I can not connect to the
website and I keep getting the "This webpage is not available" message in
my browser (
