Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

2024-06-06 Thread Eleanor Dodson 
Well, REFMAC output a (mislabelled)  F SIGF which was detwinned so if you
deposited the REFMAC output I guess that is detwinned..
Do you have the original REFMAC input still?
Eleanor

On Thu, 6 Jun 2024 at 15:18, Ben Bax  wrote:

> Hi,
>   I am just re-refining an old twinned dataset - which I will
> redeposit (refinement is never finished).
> The pdb seem to have automagically detwinned my data.
> Where do I find my original twinned data (F and SIGF)? (or will I have
> to redeposit my original un-detwinned structure factors).
>  Thanks, Ben
>
>
>
> On Fri, May 31, 2024 at 4:36 PM Ezra Peisach
>  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 i...@rcsb.org.
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
> > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
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> 
>
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Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

2024-06-06 Thread Deborah Harrus 

Dear Jon,

We will continue to serve the maps and are looking into updating the 
process to use the map coefficients now available in the wwPDB FTP data 
to make the maps compatible with the validation process.


Kind regards,

Deborah Harrus

PDBe

On 01/06/2024 14:28, 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.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android


 Original Message 
On 31/05/2024 16:36, Ezra Peisach 
 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 i...@rcsb.org.
  
  
  
  To unsubscribe from the CCP4BB list, click the following link:

  https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
  
  This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
  



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--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



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Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

2024-06-06 Thread Ben Bax 
Hi,
  I am just re-refining an old twinned dataset - which I will
redeposit (refinement is never finished).
The pdb seem to have automagically detwinned my data.
Where do I find my original twinned data (F and SIGF)? (or will I have
to redeposit my original un-detwinned structure factors).
 Thanks, Ben



On Fri, May 31, 2024 at 4:36 PM Ezra Peisach
 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 i...@rcsb.org.
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
> https://www.jiscmail.ac.uk/policyandsecurity/



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Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

2024-06-01 Thread Ezra Peisach 
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.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android


 Original Message 
On 31/05/2024 16:36, Ezra Peisach 
 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 i...@rcsb.org.
  
  
  
  To unsubscribe from the CCP4BB list, click the following link:

  https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
  
  This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
  




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Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

2024-06-01 Thread Paul Emsley 

On 01/06/2024 14:28, Jon Cooper wrote:

It would be interesting to know if this will affect the the electron density 
maps which are downloadable from the EBI:


PDBe is to RCSB as DVLA is to HMRC (surely?)



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Re: [ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

2024-06-01 Thread Jon Cooper 
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.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android


 Original Message 
On 31/05/2024 16:36, Ezra Peisach 
 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 i...@rcsb.org.
>  
>  
>  
>  To unsubscribe from the CCP4BB list, click the following link:
>  https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>  
>  This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
> https://www.jiscmail.ac.uk/policyandsecurity/
>



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[ccp4bb] Announcements: Impact of EDMAPS.rcsb.org shutdown and related June 13 Virtual Office Hour on Generating DSN6 and MTZ Files

2024-05-31 Thread Ezra Peisach 
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 i...@rcsb.org.




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