RCSB PDB is independent of PDBe with regards to this. The PDB archive
does not distribute electron density maps. Each site can provide
"feature added" data content from their websites.
As you mentioned, PDBe runs a service that uses urls like
https://www.ebi.ac.uk/pdbe/entry-files/1o08.ccp4 which is based on a
re-implementation of the legacy EDS service at Uppsala. While I cannot
speak for PDBe, I have no reason to believe that this service will be
discontinued in the near future.
Both RCSB PDB and PDBe provide electron density volumes in BinaryCif
format using a volume server. These are used by Mol* on each of their
sites. The goal for RCSB PDB is to serve up the electron density map
contents based on the maps calculated by the validation process and not
a separate process using the program DCC. Validation report map
coefficients are available for almost all X-ray structures in the PDB
archive. As software, such as Gemmi, makes it relatively
straightforward for a user o convert the PDBx/mmCIF map coefficients to
MTZ files or directly to a map, it no longer requires a large software
installation.
I believe CCP4 maps are used for much of the graphical software.
However, if you need to convert to a DSN6 file, you could use old MAPMAN
binaries, use xdlmapman (part of CCP4), sftools (part of CCP4) or
compile mapman yourself using sources at
https://github.com/martynwinn/Uppsala-Software-Factory. Up until know
RCSB PDB has produced DSN6 formatted maps using an old MAPMAN binary.
I hope this clarifies the direction we are going in.
On 6/1/24 9:28 AM, Jon Cooper wrote:
It would be interesting to know if this will affect the the electron density
maps which are downloadable from the EBI:
www.ebi.ac.uk/pdbe
They don't currently serve the older dsn6 format, only ccp4, I think.
Best wishes, Jon Cooper.
[email protected]
Sent from Proton Mail Android
-------- Original Message --------
On 31/05/2024 16:36, Ezra Peisach
<[email protected]> wrote:
In fall of 2024, electron density map coefficients will be available in
the public PDB archive for all X-ray structures. These map coefficients
will be the same as used in wwPDB Validation Reports.
The new map coefficients files will replace the electron density maps
and combined map coefficient files calculated and distributed by RCSB
PDB and used by the NGLviewer at RCSB.org. These data (served by
EDMAPS.rcsb.org) are calculated using publicly-available coordinate
files and structure factor files and offered in DSN6 formatted map files
and MTZ formatted map coefficient files. RCSB PDB plans to shutdown the
NGL viewer by July 2024
(https://www.rcsb.org/news/feature/65b42d3fc76ca3abcc925d15) and will no
longer need the data served by EDMAPS.rcsb.org.
RCSB PDB will be phasing out EDMAPS.rcsb.org:
* June 28, 2024: DSN6-formatted map files will no longer be
provided. EDMAPS.rcsb.org will only serve MTZ files with map coefficients.
* Fall 2024: Electron density map coefficients will be available
in the public PDB archive for all X-ray structures. At this point,
EDMAPS.rcsb.org will be shut down, including access to MTZ files with
map coefficients from this service.
To help users with this transition, RCSB PDB will be holding a Virtual
Office Hour on Thursday June 13, 2024 from 1:00pm-2:00pm Eastern,
10:00am-11am Pacific. Please register online for this event at
https://go.rutgers.edu/psx4pr63.
Questions about this transition or the Virtual Office Hour can be sent
to [email protected].
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