Re: [ccp4bb] Alternative ways to get electron density map other than EDS server

[Gerard DVD Kleywegt]

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 connect to the
website and I keep getting the "This webpage is not available" message in
my browser (Internet connection is ok).  I also tried to go to PDB
databank, search a structure and click "EDS" link, but this did not connect
to the server neither.

Are there other ways to get electron density maps?

Thanks.


Xiao




Best wishes,

--Gerard

**
   Gerard J. Kleywegt

  http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
**
   The opinions in this message are fictional.  Any similarity
   to actual opinions, living or dead, is purely coincidental.
**
   Little known gastromathematical curiosity: let "z" be the
   radius and "a" the thickness of a pizza. Then the volume
of that pizza is equal to pi*z*z*a !
**

Re: [ccp4bb] Alternative ways to get electron density map other than EDS server

[Donald Damian Raymond]

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 
the cif file to an MTZ using CIF2MTZ and then calculates map coefficients using 
REFMAC5. After it's done you have a PDB and MTZ you can use in any graphics 
program like PyMOL or COOT.
If you use the O graphics program by Alwyn Jones, use the follow script
https://github.com/donaldraymond/crystallography-scripts/blob/master/O_pdb.sh

It does the same as the script above, but also makes DSN6 maps and custom O 
macros. After running the script just launch O and the PDB and maps will 
automatically be loaded. 

I hope this helps. I also have a few other crystallography scripts in my github 
repo you may find useful.

Best,
Donald

.
Donald Damian Raymond, Ph.D.
Postdoctoral Research Fellow
Stephen C. Harrison Lab
Harvard Medical School
CLSB 3082
email: raym...@crystal.harvard.edu
http://www.linkedin.com/in/donalddraymond/

On Jun 9, 2015, at 4:11 PM, 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 connect to the 
> website and I keep getting the "This webpage is not available" message in my 
> browser (Internet connection is ok).  I also tried to go to PDB databank, 
> search a structure and click "EDS" link, but this did not connect to the 
> server neither.
> 
> Are there other ways to get electron density maps?
> 
> Thanks.
> 
> 
> Xiao

Re: [ccp4bb] Alternative ways to get electron density map other than EDS server

[georg mlynek]

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. 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, 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
connect to the website and I keep getting the "This webpage is not
available" message in my browser (Internet connection is ok).  I
also tried to go to PDB databank, search a structure and click
"EDS" link, but this did not connect to the server neither.

Are there other ways to get electron density maps?

Thanks.


Xiao

Re: [ccp4bb] Alternative ways to get electron density map other than EDS server

[Dale Tronrud]

   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 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 connect to
> the website and I keep getting the "This webpage is not available"
> message in my browser (Internet connection is ok).  I also tried to go
> to PDB databank, search a structure and click "EDS" link, but this did
> not connect to the server neither.
> 
> Are there other ways to get electron density maps?
> 
> Thanks.
> 
> 
> Xiao

Re: [ccp4bb] Alternative ways to get electron density map other than EDS server

[Pavel Afonine]

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, 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 connect to
> the website and I keep getting the "This webpage is not available" message
> in my browser (Internet connection is ok).  I also tried to go to PDB
> databank, search a structure and click "EDS" link, but this did not connect
> to the server neither.
>
> Are there other ways to get electron density maps?
>
> Thanks.
>
>
> Xiao
>

Re: [ccp4bb] Alternative ways to get electron density map other than EDS server

[Tim Gruene]

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,
> 
> 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 (Internet connection is ok).  I also tried to go to PDB
> databank, search a structure and click "EDS" link, but this did not connect
> to the server neither.
> 
> Are there other ways to get electron density maps?
> 
> Thanks.
> 
> 
> Xiao

-- 
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
phone: +49 (0)551 39 22149

GPG Key ID = A46BEE1A

[ccp4bb] Alternative ways to get electron density map other than EDS server

[Xiao Lei]

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 (Internet connection is ok).  I also tried to go to PDB
databank, search a structure and click "EDS" link, but this did not connect
to the server neither.

Are there other ways to get electron density maps?

Thanks.


Xiao