Re: [ccp4bb] Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive

[Eleanor Dodson]

This is excellent news - we have a series of related structures solved in
the YSBL - several sets of which are on different crystallographic origins.
It doesnt matter of course crystallographically but is confusing for
comparison..
Now we can alter them to a common origin with redepositing the information..
Eleanor Dodson

On 18 May 2017 at 15:22, Jasmine Young  wrote:

> Hi Ed,
>
> The PDB accession code will be based on the primary data stored in the
> PDB.  Therefore depositors will need to make a new deposition with new PDB
> accession code issued if the atomic coordinates are modified using newly
> processed intensities from the original diffraction images.
>
> More details on the procedure will be made available at a later date.
>
>
> Regards,
>
> Jasmine
>
> ===
> Jasmine Young, Ph.D.
> Biocuration Team Lead
> RCSB Protein Data Bank
> Associate Research Professor
> Center for Integrative Proteomics Research
> Rutgers, The State University of New Jersey
> 174 Frelinghuysen Rd
> Piscataway, NJ 08854-8087
>
> Email: jasm...@rcsb.rutgers.edu
> Phone: (848)445-0103 ext 4920
> Fax: (732)445-4320
> ===
>
> On 5/17/17 12:11 PM, Edward A. Berry wrote:
>
>> Couple of wuestions:
>> What is the procedure for updating an entry? Start a new submission, or
>> mail revised coordinates along with an explanation of changes to
>> deposit@rcsb?
>>
>> "unchanged experimental data" - does this mean the exact same structure
>> factors, or will newly reduced data from the same original diffraction
>> images be acceptable?
>>
>> Thanks,
>> Ed
>>
>> On 05/17/2017 09:28 AM, Jasmine Young wrote:
>>
>>> *Use CAUTION opening attachments or clicking on links in emails - IMT
>>> Help Desk, 4-4115*
>>>
>>>
>>>
>>> The wwPDB is planning to introduce in 2017 a new procedure for the
>>> management by the Depositor of Record (where the Depositor of Record is
>>> defined as the Principal Investigator for the entry) of substantial
>>> revisions to previously released PDB archival entries.
>>>
>>> At present, revised atomic coordinates for an existing released PDB
>>> entry are assigned a new accession code, and the prior entry is obsoleted.
>>> This long-standing wwPDB policy had the unintended consequence of breaking
>>> connections with publications and usage of the prior set of atomic
>>> coordinates, resulting in a non-trivial barrier to submission of atomic
>>> coordinate revisions by our Depositors of Record.
>>>
>>> The wwPDB is introducing a file versioning system that allows Depositors
>>> of Record to update their own previously released entries. Please note, in
>>> the first phase, file versioning will be applied to the atomic coordinates
>>> refined versus unchanged experimental data.
>>>
>>> Version numbers of each PDB archive entry will be designated using a #-#
>>> identifier. The first digit specifies the major version, and the second
>>> designates the minor version. The Structure of Record (i.e., the initial
>>> set of released atomic coordinates) is designated as Version 1-0.
>>> Thereafter, the major version digit is incremented with each substantial
>>> revision of a given entry (e.g., Version 2-0, when the atomic coordinates
>>> are replaced for the first time by the Depositor of Record). “Major version
>>> changes” are defined as updates to the atomic coordinates, polymer
>>> sequence(s), and/or chemical identify of a ligand. All other changes are
>>> defined as “minor changes”. When a major change is made, the minor version
>>> number is reset to 0 (e.g., 1-0 to 1-1 to 2-0). For the avoidance of doubt,
>>> the wwPDB will retain all major versions with the latest minor versions of
>>> an entry within the PDB archive.
>>>
>>> Current wwPDB policies governing the deposition of independently refined
>>> structures based on the data generated by a research group or laboratory
>>> separate from that of the Depositor of Record remain unchanged. Versioning
>>> of atomic coordinates will be strictly limited to substitutions made by the
>>> Depositor of Record.
>>>
>>> Upon introduction of the file versioning system, the wwPDB will revise
>>> each PDB accession code by extending its length and prepending “PDB” (e.g.,
>>> "1abc" will become "pdb_1abc"). This process will enable text mining
>>> detection of PDB entries in the published literature and allow for more
>>> informative and transparent delivery of revised data files. For example,
>>> the atomic coordinates for the second major version of PDB entry 1abc would
>>> have the following form under the new file-naming schema:
>>>
>>> pdb_1abc_xyz_v2-0.cif.gz
>>>
>>> The wwPDB is mindful of the importance of continuity in providing
>>> services and supporting User activities. For as long as practicable, the
>>> wwPDB will continue assigning PDB codes that can be truncated losslessly to
>>> the current four-character style. In the 

Re: [ccp4bb] Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive

[Jasmine Young]

Hi Ed,

The PDB accession code will be based on the primary data stored in the 
PDB.  Therefore depositors will need to make a new deposition with new 
PDB accession code issued if the atomic coordinates are modified using 
newly processed intensities from the original diffraction images.


More details on the procedure will be made available at a later date.


Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Associate Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

On 5/17/17 12:11 PM, Edward A. Berry wrote:

Couple of wuestions:
What is the procedure for updating an entry? Start a new submission, 
or mail revised coordinates along with an explanation of changes to 
deposit@rcsb?


"unchanged experimental data" - does this mean the exact same 
structure factors, or will newly reduced data from the same original 
diffraction images be acceptable?


Thanks,
Ed

On 05/17/2017 09:28 AM, Jasmine Young wrote:
*Use CAUTION opening attachments or clicking on links in emails - IMT 
Help Desk, 4-4115*




The wwPDB is planning to introduce in 2017 a new procedure for the 
management by the Depositor of Record (where the Depositor of Record 
is defined as the Principal Investigator for the entry) of 
substantial revisions to previously released PDB archival entries.


At present, revised atomic coordinates for an existing released PDB 
entry are assigned a new accession code, and the prior entry is 
obsoleted. This long-standing wwPDB policy had the unintended 
consequence of breaking connections with publications and usage of 
the prior set of atomic coordinates, resulting in a non-trivial 
barrier to submission of atomic coordinate revisions by our 
Depositors of Record.


The wwPDB is introducing a file versioning system that allows 
Depositors of Record to update their own previously released entries. 
Please note, in the first phase, file versioning will be applied to 
the atomic coordinates refined versus unchanged experimental data.


Version numbers of each PDB archive entry will be designated using a 
#-# identifier. The first digit specifies the major version, and the 
second designates the minor version. The Structure of Record (i.e., 
the initial set of released atomic coordinates) is designated as 
Version 1-0. Thereafter, the major version digit is incremented with 
each substantial revision of a given entry (e.g., Version 2-0, when 
the atomic coordinates are replaced for the first time by the 
Depositor of Record). “Major version changes” are defined as updates 
to the atomic coordinates, polymer sequence(s), and/or chemical 
identify of a ligand. All other changes are defined as “minor 
changes”. When a major change is made, the minor version number is 
reset to 0 (e.g., 1-0 to 1-1 to 2-0). For the avoidance of doubt, the 
wwPDB will retain all major versions with the latest minor versions 
of an entry within the PDB archive.


Current wwPDB policies governing the deposition of independently 
refined structures based on the data generated by a research group or 
laboratory separate from that of the Depositor of Record remain 
unchanged. Versioning of atomic coordinates will be strictly limited 
to substitutions made by the Depositor of Record.


Upon introduction of the file versioning system, the wwPDB will 
revise each PDB accession code by extending its length and prepending 
“PDB” (e.g., "1abc" will become "pdb_1abc"). This process will 
enable text mining detection of PDB entries in the published 
literature and allow for more informative and transparent delivery of 
revised data files. For example, the atomic coordinates for the 
second major version of PDB entry 1abc would have the following form 
under the new file-naming schema:


pdb_1abc_xyz_v2-0.cif.gz

The wwPDB is mindful of the importance of continuity in providing 
services and supporting User activities. For as long as practicable, 
the wwPDB will continue assigning PDB codes that can be truncated 
losslessly to the current four-character style. In the same spirit, 
initial implementation of entry file versioning will appear in a new, 
parallel branch of the PDB archive FTP tree. More details on the new 
FTP tree organization and accessibility of version information will 
be forthcoming. Data files in the current archive location 
ftp://ftp.wwpdb.org/pub/pdb/data/structures/ will continue to use the 
familiar naming style and will contain the latest version in the 
corresponding versioned archive.





--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein 

Re: [ccp4bb] Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive

[Edward A. Berry]

Couple of wuestions:
What is the procedure for updating an entry? Start a new submission, or mail 
revised coordinates along with an explanation of changes to deposit@rcsb?

"unchanged experimental data" - does this mean the exact same structure 
factors, or will newly reduced data from the same original diffraction images be 
acceptable?

Thanks,
Ed

On 05/17/2017 09:28 AM, Jasmine Young wrote:

*Use CAUTION opening attachments or clicking on links in emails - IMT Help 
Desk, 4-4115*



The wwPDB is planning to introduce in 2017 a new procedure for the management 
by the Depositor of Record (where the Depositor of Record is defined as the 
Principal Investigator for the entry) of substantial revisions to previously 
released PDB archival entries.

At present, revised atomic coordinates for an existing released PDB entry are 
assigned a new accession code, and the prior entry is obsoleted. This 
long-standing wwPDB policy had the unintended consequence of breaking 
connections with publications and usage of the prior set of atomic coordinates, 
resulting in a non-trivial barrier to submission of atomic coordinate revisions 
by our Depositors of Record.

The wwPDB is introducing a file versioning system that allows Depositors of 
Record to update their own previously released entries. Please note, in the 
first phase, file versioning will be applied to the atomic coordinates refined 
versus unchanged experimental data.

Version numbers of each PDB archive entry will be designated using a #-# 
identifier. The first digit specifies the major version, and the second 
designates the minor version. The Structure of Record (i.e., the initial set of 
released atomic coordinates) is designated as Version 1-0. Thereafter, the 
major version digit is incremented with each substantial revision of a given 
entry (e.g., Version 2-0, when the atomic coordinates are replaced for the 
first time by the Depositor of Record). “Major version changes” are defined as 
updates to the atomic coordinates, polymer sequence(s), and/or chemical 
identify of a ligand. All other changes are defined as “minor changes”. When a 
major change is made, the minor version number is reset to 0 (e.g., 1-0 to 1-1 
to 2-0). For the avoidance of doubt, the wwPDB will retain all major versions 
with the latest minor versions of an entry within the PDB archive.

Current wwPDB policies governing the deposition of independently refined 
structures based on the data generated by a research group or laboratory 
separate from that of the Depositor of Record remain unchanged. Versioning of 
atomic coordinates will be strictly limited to substitutions made by the 
Depositor of Record.

Upon introduction of the file versioning system, the wwPDB will revise each PDB accession code by 
extending its length and prepending “PDB” (e.g., "1abc" will become 
"pdb_1abc"). This process will enable text mining detection of PDB entries in the 
published literature and allow for more informative and transparent delivery of revised data files. 
For example, the atomic coordinates for the second major version of PDB entry 1abc would have the 
following form under the new file-naming schema:

pdb_1abc_xyz_v2-0.cif.gz

The wwPDB is mindful of the importance of continuity in providing services and 
supporting User activities. For as long as practicable, the wwPDB will continue 
assigning PDB codes that can be truncated losslessly to the current 
four-character style. In the same spirit, initial implementation of entry file 
versioning will appear in a new, parallel branch of the PDB archive FTP tree. 
More details on the new FTP tree organization and accessibility of version 
information will be forthcoming. Data files in the current archive location 
ftp://ftp.wwpdb.org/pub/pdb/data/structures/ will continue to use the familiar 
naming style and will contain the latest version in the corresponding versioned 
archive.




--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Associate Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email:jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

[ccp4bb] Revise Your Structure Without Changing the PDB Accession Code and Related Changes to the FTP Archive

[Jasmine Young]

The wwPDB is planning to introduce in 2017 a new procedure for the 
management by the Depositor of Record (where the Depositor of Record is 
defined as the Principal Investigator for the entry) of substantial 
revisions to previously released PDB archival entries.


At present, revised atomic coordinates for an existing released PDB 
entry are assigned a new accession code, and the prior entry is 
obsoleted. This long-standing wwPDB policy had the unintended 
consequence of breaking connections with publications and usage of the 
prior set of atomic coordinates, resulting in a non-trivial barrier to 
submission of atomic coordinate revisions by our Depositors of Record.


The wwPDB is introducing a file versioning system that allows Depositors 
of Record to update their own previously released entries. Please note, 
in the first phase, file versioning will be applied to the atomic 
coordinates refined versus unchanged experimental data.


Version numbers of each PDB archive entry will be designated using a #-# 
identifier. The first digit specifies the major version, and the second 
designates the minor version. The Structure of Record (i.e., the initial 
set of released atomic coordinates) is designated as Version 1-0. 
Thereafter, the major version digit is incremented with each substantial 
revision of a given entry (e.g., Version 2-0, when the atomic 
coordinates are replaced for the first time by the Depositor of Record). 
“Major version changes” are defined as updates to the atomic 
coordinates, polymer sequence(s), and/or chemical identify of a ligand. 
All other changes are defined as “minor changes”. When a major change is 
made, the minor version number is reset to 0 (e.g., 1-0 to 1-1 to 2-0). 
For the avoidance of doubt, the wwPDB will retain all major versions 
with the latest minor versions of an entry within the PDB archive.


Current wwPDB policies governing the deposition of independently refined 
structures based on the data generated by a research group or laboratory 
separate from that of the Depositor of Record remain unchanged. 
Versioning of atomic coordinates will be strictly limited to 
substitutions made by the Depositor of Record.


Upon introduction of the file versioning system, the wwPDB will revise 
each PDB accession code by extending its length and prepending “PDB” 
(e.g., "1abc" will become "pdb_1abc"). This process will enable text 
mining detection of PDB entries in the published literature and allow 
for more informative and transparent delivery of revised data files. For 
example, the atomic coordinates for the second major version of PDB 
entry 1abc would have the following form under the new file-naming schema:


pdb_1abc_xyz_v2-0.cif.gz

The wwPDB is mindful of the importance of continuity in providing 
services and supporting User activities. For as long as practicable, the 
wwPDB will continue assigning PDB codes that can be truncated losslessly 
to the current four-character style. In the same spirit, initial 
implementation of entry file versioning will appear in a new, parallel 
branch of the PDB archive FTP tree. More details on the new FTP tree 
organization and accessibility of version information will be 
forthcoming. Data files in the current archive location 
ftp://ftp.wwpdb.org/pub/pdb/data/structures/ will continue to use the 
familiar naming style and will contain the latest version in the 
corresponding versioned archive.





--
Regards,

Jasmine

===
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Associate Research Professor
Center for Integrative Proteomics Research
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087

Email: jasm...@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
===

Re: [ccp4bb] Revise

[Stein, ND (Norman)]

Dear Sajid

It sound as though you are running Revise through CCP4i. If you do this,
the first thing you normally select is your mtz file. The buttons
labelled 'FPH+1' and 'FPH-1' in the gui then default to the same thing.
You need to click on at least one of these buttons and select a
different label. You should then no longer get duplicate column labels
in your output file.

Norman

Norman Stein
CCP4
Daresbury Laboratory
Warrington
WA4 4AD
UK  

-Original Message-
From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of
sajid akthar
Sent: 15 April 2008 19:03
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Revise

Dear All

I'm trying to locate heavy atoms. SO I started with Revise from CCP4.
But it fails with error message

#CCP4I TERMINATION STATUS 0  REVISE:  Duplicate column labels in output
file
#CCP4I TERMINATION TIME 15 Apr 2008  14:50:34 #CCP4I MESSAGE Task failed


Any help pls

Thanks
Sajid


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