Dear Marcin,
Thank you for your feedback. We will improve mmCIF documentation for
this recommendation.
Most of the wwPDB remediation do not require change of chain id or
residue numbering. For new data representation such as carbohydrates and
previous remediation of peptide-like inhibitors,
Dear Jasmine,
I fully agree with this recommendation:
> To use the wwPDB-assigned chain ID in publications,
> _atom_site.auth_seq_id _atom_site.auth_comp_id, and
> _atom_site.auth_asym_id can be used for the residue number, residue ID,
> and chain ID, respectively.
It would help a lot if the sam
Dear Jasmine,
Thank you for contributing to this thread.
This has been asked in a different way, but can we simply assume at this
point that the mmCIF/PDB records will no longer contain any or separate
chain ID-like item that reflects chains including proteins and their
glycans, as has been t
Dear Marcin,
The cif item, _pdbx_branch_scheme.pdb_asym_id, in the pdbx_branch_scheme
category is a pointer to _atom_site.auth_asym_id in the atom_site
category (I know this is confusing). The labels are consistently defined
as the ones in _pdbx_poly_seq_scheme and _pdbx_nonpoly_scheme.
To u
Dear Jasmine,
thank you for this explanation. It's the best explanation of this
remediation I've read.
The use of IDs may confuse people, so I'd like to reiterate it and ask
for clarification.
Every residue in the mmCIF format has three (3) independent chain IDs
assigned to it (and three sequence
: [ccp4bb] Coming July 29: Improved Carbohydrate Data at
the PDB -- N-glycans are now separate chains if more than one residue
Dear PDB Data Users:
Thank you for providing feedback on the results of an archival-level
carbohydrate remediation project that led to the re-release of over
14,000 PDB
, December 8, 2020 21:01
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB --
N-glycans are now separate chains if more than one residue
Dear PDB Data Users:
Thank you for providing feedback on the results of an archival-level
carbohydrate remediation
Dear PDB Data Users:
Thank you for providing feedback on the results of an archival-level
carbohydrate remediation project that led to the re-release of over
14,000 PDB structures in July 2020. This update includes diverse
oligosaccharides: glycosylation; metabolites such as maltose, sucrose,
We have drifted far from the original topic of this thread and if we
continue I'll just make more of a fool of myself.
I'll just go back to the original topic that I started with, that
encoding connectivity information into an ID is not reliable or
sustainable in a relational database.
On Fri, 4 Dec 2020 at 22:36, Dale Tronrud wrote:
>
> It is very important not to read more meaning into a data tag than
> is actually defined in the mmCIF spec. _atom_site.label_seq_id is defined
>
> http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_atom_site.label_seq_id.html
>
>
On 12/4/2020 12:15 PM, Marcin Wojdyr wrote:
> On Fri, 4 Dec 2020 at 19:16, Dale Tronrud wrote:
>> learn the sequence you have to go to the mmCIF records that define the
>> connectivity between residues. It is entirely possible that "3" comes
>> before "1" because these indexes don't contain any
On Fri, 4 Dec 2020 at 19:16, Dale Tronrud wrote:
>
> Creating meaning in the chain names "A, B, C, Ag1, Ag2, Ag3" is
> exactly the problem.
It's not about "creating meaning" but about consistent naming. For humans.
> "chain names" ( or "entity identifiers" if I
> recall the mmCIF terminology
ember 2020 18:16
*To:* Tristan Croll ; CCP4BB@JISCMAIL.AC.UK
*Subject:* Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at
the PDB -- N-glycans are now separate chains if more than one residue
Creating meaning in the chain names "A, B, C, Ag1, Ag2, Ag3" is
exactly the p
: CCP4 bulletin board On Behalf Of Dale
> Tronrud
> Sent: Friday, December 4, 2020 19:16
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the
> PDB -- N-glycans are now separate chains if more than one residue
>
> Creating meani
: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the
PDB -- N-glycans are now separate chains if more than one residue
mmCIF has two different chain ids. One the the label_asym_id which is
used for internal consistency with the entities. The other is the
auth_asym_id which is whatever t
other fields.
Cheers,
Robbie
> -Original Message-
> From: CCP4 bulletin board On Behalf Of Luca
> Jovine
> Sent: Friday, December 4, 2020 18:45
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the
> PDB -- N-glycans are n
end user in mind when
making decisions like this.
From: Dale Tronrud
Sent: 04 December 2020 18:16
To: Tristan Croll ; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB --
N-glycans are now separate chains if more than one residue
not necessarily mean that the protein was treated by endoH. In
fact all sites are extended to at least tri-Man in most cases. Then why
keeping some sites associated with the protein chain while others kicked
out?
Zhijie
________
From: CCP4 bulletin board on behalf of John
Berrisford
Sent: Thurs
"A, B, C, Ag1, Ag2, Ag3", then we have something that is far more immediately
> accessible to the user.
>
>
> From: Dale Tronrud
> Sent: 04 December 2020 17:01
> To: Tristan Croll ; CCP4BB@JISCMAIL.AC.UK
>
> Subject: Re: [ccp4bb] Coming July 29: Improved
s were something like "A, B, C,
Ag1, Ag2, Ag3", then we have something that is far more immediately accessible
to the user.
From: Dale Tronrud
Sent: 04 December 2020 17:01
To: Tristan Croll ; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coming July 2
N- or O-glycosylation sites as
>>> these might change during model building or, in my case, carbohydrate
>>> rebuilding in PDB-REDO powered by Coot. Thanks for pointing this out.
>>>
>>> Cheers,
>>> Robbie
>>>
>>>> -Original Messa
g model building or, in my case, carbohydrate rebuilding in PDB-REDO powered by Coot. Thanks for pointing this out.
>>>
>>> Cheers,
>>> Robbie
>>>
>>>> -----Original Message-
>>>> From: CCP4 bulletin board On Behalf Of Zhijie Li
>>>
this out.
Cheers,
Robbie
-Original Message-
From: CCP4 bulletin board On Behalf Of Zhijie Li
Sent: Thursday, December 3, 2020 19:52
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the
PDB -- N-glycans are now separate chains if more tha
On Fri, 4 Dec 2020 at 09:21, Luca Jovine wrote:
>
> Yes Tristan, that would be even better - also because such an Ag1, Ag2,…
> system could conveniently fall back on a single-character chain A, when
> generating legacy PDB format files from the mmCIF ones.
mmCIF already has two sets of identifi
ebuilding in PDB-REDO powered by Coot. Thanks for pointing this out.
>>>
>>> Cheers,
>>> Robbie
>>>
>>>> -Original Message-----
>>>> From: CCP4 bulletin board On Behalf Of Zhijie Li
>>>> Sent: Thursday, December 3, 2
model building or, in my case, carbohydrate
>>> rebuilding in PDB-REDO powered by Coot. Thanks for pointing this out.
>>>
>>> Cheers,
>>> Robbie
>>>
>>>> -Original Message-
>>>> From: CCP4 bulletin board On Behalf Of Zh
ylation sites as
>>> these might change during model building or, in my case, carbohydrate
>>> rebuilding in PDB-REDO powered by Coot. Thanks for pointing this out.
>>>
>>> Cheers,
>>> Robbie
>>>
>>>> -Original Message-
>
ks for pointing this out.
>>
>> Cheers,
>> Robbie
>>
>>> -Original Message-
>>> From: CCP4 bulletin board On Behalf Of Zhijie Li
>>> Sent: Thursday, December 3, 2020 19:52
>>> To: CCP4BB@JISCMAIL.AC.UK
>>> Subje
pointing this out.
> >
> > Cheers,
> > Robbie
> >
> >> -Original Message-
> >> From: CCP4 bulletin board On Behalf Of Zhijie
> Li
> >> Sent: Thursday, December 3, 2020 19:52
> >> To: CCP4BB@JISCMAIL.AC.UK
> >> Subjec
bulletin board On Behalf Of Zhijie Li
>> Sent: Thursday, December 3, 2020 19:52
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the
>> PDB -- N-glycans are now separate chains if more than one residue
>>
>> Hi all,
&g
t;
> Zhijie
>
>
>
> ____________
>
> From: CCP4 bulletin board on behalf of John
> Berrisford
> Sent: Thursday, July 9, 2020 4:39 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB
>
ed out?
Zhijie
From: CCP4 bulletin board on behalf of John Berrisford
Sent: Thursday, July 9, 2020 4:39 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB
Dear CCP4BB
PDB data will shortly incorporate a new data rep
Dear CCP4BB
PDB data will shortly incorporate a new data representation for
carbohydrates in PDB entries and reference data that improves the
Findability and Interoperability of these molecules in macromolecular
structures. In order to remediate and improve the representation of
carbohydrates acro
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