On 27/05/14 22:42, RiC wrote:
HI,
Does anyone have a step by step guide to go from a structure factor file from
the PDB to a CCP4 map (understandable to a biologist) like the one I can
download on the electron density server?
Hi Patrick,
Depending on the program with which you will view the output of the EDS,
you may or may not need to use a map. Let's presume that you will use
Coot (and so you will not need the map (and thus not need to run fft to
make it)).
I use Extensions -> PDBe -> Get from PDBe -> "1c75" -> Get It
If that fails (it does occasionally/rarely) then I use File -> Fetch PDB
and Map from EDS...
Coot runs refmac5 (with 0 cycles) when using the former but not the
latter. In the EDS case, Coot also scrapes the relevant web page to let
you know if EDS thought that the map was "unreliable."
You may also be interested in File -> Fetch PDB and Map using PDB_REDO,
which also displays a map - but a someone different one.
The conversation has been an eye-opener.
Paul.
