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: [email protected] http://www.linkedin.com/in/donalddraymond/ On Jun 9, 2015, at 4:11 PM, Xiao Lei <[email protected]> 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
