Does RCSB discontinuing edsmap.rcsb.org effect or EDS fetch

[meng@…]

From: Elaine Meng
Subject: do we use RCSB ED maps?
Date: May 28, 2024 at 11:06:39 AM PDT
To: Chimera Staff

I don't remember seeing anything forwarded from the rest of the team about this, so in case it's relevant (Fetch by ID?). Apologies if we have discussed it and I just forgot:

Announcement: EDMAPS.rcsb.org Shutdown

05/09

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 distributed by RCSB PDB and used by the NGLviewer at RCSB.org. These data (currently 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 (announcement) 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 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.

[Tom Goddard]

The PDBe help desk says they will continues to provide the EDS maps that ChimeraX fetches. The RCSB announcement about discontinuing edsmaps.rcsb.org does not effect ChimeraX because we do not use that source for fetching maps.

From: "Genevieve Evans via RT" <pdbehelp@…>
Subject: [PDBe #743974] Electron Density Server
Date: May 29, 2024 at 7:43:53 AM PDT
To: goddard

<URL: http://helpdesk.ebi.ac.uk/Ticket/Display.html?id=743974 >

Hi Tom,

We (PDBe) will continue to produce real-space X-ray (electron density) maps.

Kind Regards,
Genevieve Evans
PDBe

I am wondering if PDBe is planning to shut down the Electron Density Server
that provides real-space X-ray maps, for example,

​http://www.ebi.ac.uk/pdbe/coordinates/files/1cbs.ccp4

I ask because of a recent RCSB announced that they will no longer provide
real-space X-ray maps in Fall of 2024. I wonder if this is a wwPDB decision,
or is just the RCSB. I develop ChimeraX which allows fetching maps from the
PDBe electron density server and I want to plan if that service will be
discontinued.

Thanks!

Tom Goddard
ChimeraX developer