OK, I understand your point more clearly now - but I'm not sure I fully agree,
for the simple reason that people aren't computers. You're right that for the
purposes of software validation tools the chain IDs are essentially arbitrary -
as long as they're unique, nothing else really matters. But to a human simply
wanting to explore a model in their favourite visualisation program this makes
everything just that bit less intuitive - if they want to, say, go to the first
glycan attached to chain A they have no way of doing so short of tracing
through from the N-terminus until they find it, unless the program provides a
tool that already understands the concept of "first glycan attached to chain
A". So if we go forward with the "chain IDs are entirely arbitrary, therefore
it doesn't matter what they are" approach, then every existing visualisation
tool gets a little bit more difficult to use with glycans until their authors
take the time to write new task-specific code.
In the grand scheme of things it's a minor issue, I suppose - but in my opinion
it really is important to keep the experience of the end user in mind when
making decisions like this.
________________________________
From: Dale Tronrud <de...@daletronrud.com>
Sent: 04 December 2020 18:16
To: Tristan Croll <ti...@cam.ac.uk>; CCP4BB@JISCMAIL.AC.UK
<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 problem. "chain names" ( or "entity identifiers" if I
recall the mmCIF terminology correctly) are simply database "indexes".
The values of indices are meaningless in themselves, they are just
unique values that can be used to unambiguously identify a record. In
principle, you could just assign random ISO characters (I don't think
mmCIF allows unicode) and the mmCIF would be considered identical.
You are trying to force meaning to the characters with an index, and
that puts multiple types of information in a single field. As Robbie
said already exists, if you want to encode connectivity into the data
base you have to add records that define that connectivity. That places
the connectivity information explicitly in the data models and allows
standard data base tools to track and validate.
The idioms of the PDB cause problems that lead people to these
mistakes. The PDB assigns the indices "1", "2", and "3" to residues in
a chain. A person could be misled into thinking that "2" comes between
"1" and "3" in the sequence. This is not necessarily true at all. To
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 information, other
than being unique within the chain.
Dale Tronrud
On 12/4/2020 9:46 AM, Tristan Croll wrote:
> This suggestion violates a basic principle of data base theory. A
> single data item cannot encode two pieces of information.
>
> I'm sorry if I was unclear, but I don't believe I was suggesting
> anything of the sort. Hopefully this example should make it more clear -
> I'm just suggesting a slight variation on the existing system, no more:
>
> If we start with model containing 3 protein chains A-C, with chain A
> containing amino acid residues 1-200, and 3 N-linked glycans with
> residues numbered, say, 1000-1005, 1020-1026 and 1040-1043 (a fairly
> common approach I've seen taken to the problem in the past, and one I've
> taken myself), then if I understand correctly after remediation we'll
> have a model with protein chains A-C and glycan chains D-F. The problem
> is, unless and until all the available visualisation software updates to
> automatically associate chains D-F to chain A based on linkage, the user
> just has to remember that chains D-F are actually the chain A glycans.
> This is a simple case, but things quickly become far more messy when you
> have multiple glycosylated species each with multiple glycans per chain.
> If, instead, the new chain assignments 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 <de...@daletronrud.com>
> *Sent:* 04 December 2020 17:01
> *To:* Tristan Croll <ti...@cam.ac.uk>; CCP4BB@JISCMAIL.AC.UK
> <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
>
> This suggestion violates a basic principle of data base theory. A
> single data item cannot encode two pieces of information. The whole
> structure of CIF falls apart if this is done.
>
> Does the new PDB convention contain a CIF record of the link that
> bridges between the protein chain and the, now separated, glycan chain?
> If not, I think this is the principle failing of their new scheme.
>
> Dale Tronrud
>
> On 12/4/2020 12:06 AM, Tristan Croll wrote:
>> To go one step further: in large, heavily glycosylated multi-chain complexes
>> the assignment of a random new chain ID to each glycan will lead to
>> headaches for people building visualisations using existing viewers, because
>> it loses the easy name-based association of glycan to parent protein chain.
>> A suggestion: why not take full
> advantage of the mmCIF capability for multi-character chain IDs, and
> name them by appending characters to the parent chain ID? Using chain A
> as an example, perhaps the glycans could become Ag1, Ag2, etc.?
>>
>>> On 4 Dec 2020, at 07:48, Luca Jovine <luca.jov...@ki.se> wrote:
>>>
>>> CC: pdb-l
>>>
>>> Dear Zhijie and Robbie,
>>>
>>> I agree with both of you that the new carbohydrate chain assignment
>>> convention that has been recently adopted by PDB introduces confusion, not
>>> just for PDB-REDO but also - and especially - for end users.
>>>
>>> Could we kindly ask PDB to improve consistency by either assigning a
>>> separate chain to all covalently attached carbohydrates (regardless of
>>> whether one or more residues have been traced), or reverting to the old
>>> system (where N-/O-glycans inherited the same chain ID of the protein to
>>> which they are attached)? The current
> hybrid solution hardly seems optimal...
>>>
>>> Best regards,
>>>
>>> Luca
>>>
>>>> On 3 Dec 2020, at 20:17, Robbie Joosten <robbie_joos...@hotmail.com> wrote:
>>>>
>>>> Dear Zhijie,
>>>>
>>>> In generally I like the treatment of carbohydrates now as branched
>>>> polymers. I didn't realise there was an exception. It makes sense for
>>>> unlinked carbohydrate ligands, but not for 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 Message-----
>>>>> From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> 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,
>>>>>
>>>>> I was confused when I saw mysterious new glycan chains emerging during
>>>>> PDB deposition and spent quite some time trying to find out what was
>>>>> wrong with my coordinates. Then it occurred to me that a lot of recent
>>>>> structures also had tens of N-glycan chains. Finally I realized that this
>>>>> phenomenon is a consequence of this PDB policy announced here in July.
>>>>>
>>>>>
>>>>> For future depositors who might also get puzzled, let's put it in a short
>>>>> sentence: O- and N-glycans are now separate chains if it they contain
>>>>> more
>>>>> than one residue; single residues remain with the protein chain.
>>>>>
>>>>>
>>>>> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wwpdb.org%2Fdocumentation%2Fcarbohydrate-remediation&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684263065%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=mBrkCJECFpZyCih4kOCcCvLT1GzQHxD5GD7bZDI9s1s%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wwpdb.org%2Fdocumentation%2Fcarbohydrate-remediation&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684263065%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=mBrkCJECFpZyCih4kOCcCvLT1GzQHxD5GD7bZDI9s1s%3D&reserved=0>
>>>>>
>>>>> "Oligosaccharide molecules are classified as a new entity type, branched,
>>>>> assigned a unique chain ID (_atom_site.auth_asym_id) and a new mmCIF
>>>>> category introduced to define the type of branching
>>>>> (_pdbx_entity_branch.type) . "
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> I found the differential treatment of single-residue glycans and
>>>>> multi-residue
>>>>> glycans not only bit lack of aesthetics but also misleading. When a
>>>>> structure
>>>>> contains both NAG-NAG... and single NAG on N-glycosylation sites, it might
>>>>> be because of lack of density for building more residues, or because that
>>>>> some of the glycosylation sites are now indeed single NAGs (endoH etc.)
>>>>> while some others are not cleaved due to accessibility issues. Leaving
>>>>> NAGs
>>>>> on the protein chain while assigning NAG-NAG... to a new chain, feels like
>>>>> suggesting something about their true oligomeric state.
>>>>>
>>>>>
>>>>> For example, for cryoEM structures, when one only builds a single NAG at a
>>>>> site does 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 <CCP4BB@JISCMAIL.AC.UK> on behalf of John
>>>>> Berrisford <j...@ebi.ac.uk>
>>>>> Sent: Thursday, July 9, 2020 4:39 AM
>>>>> To: CCP4BB@JISCMAIL.AC.UK <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 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 across the archive, the wwPDB has:
>>>>>
>>>>> *standardized Chemical Component Dictionary nomenclature
>>>>> following IUPAC-IUBMB recommendations
>>>>> *provided uniform representation for oligosaccharides
>>>>> *adopted Glycoscience-community commonly used linear descriptors
>>>>> using community tools
>>>>> *annotated glycosylation sites in PDB structures
>>>>>
>>>>> Starting July 29, 2020, users will be able to access the improved data
>>>>> via FTP
>>>>> or wwPDB partner websites. Detailed information about this project is
>>>>> available at the wwPDB website
>>>>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wwpdb.org%2Fdocumentation%2Fcarbohydrate-remediation&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6begIrz7OgNq8CecxMhAhm3n%2F4WPAMM%2F4dg9uwmlrcs%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wwpdb.org%2Fdocumentation%2Fcarbohydrate-remediation&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6begIrz7OgNq8CecxMhAhm3n%2F4WPAMM%2F4dg9uwmlrcs%3D&reserved=0>>
> ; lists
>>>>> of impacted entries and chemical components will be published on this page
>>>>> after data release.
>>>>>
>>>>> The wwPDB has created a new ‘branched’ entity representation for
>>>>> polysaccharides, describing all the individual monosaccharide components
>>>>> of
>>>>> these in the PDB entry. As part of this process, we have standardized atom
>>>>> nomenclature of >1,000 monosaccharides in the Chemical Component
>>>>> Dictionary (CCD) and applied a branched entity representation to
>>>>> oligosaccharides for >8000 PDB entries. To guarantee unambiguous chemical
>>>>> description of oligosaccharides in the affected PDB entries, an explicit
>>>>> description of covalent linkage information between their monosaccharide
>>>>> units is included. In addition, wwPDB validation reports provide
>>>>> consistent
>>>>> representation for these oligosaccharides and include 2D representations
>>>>> based on the Symbol Nomenclature for Glycans (SNFG).
>>>>>
>>>>> To support the remediation of carbohydrate representation, software tools
>>>>> providing linear descriptors were developed in collaboration with the
>>>>> glycoscience community to enable easy translation of PDB data to other
>>>>> representations commonly used by glycobiologists. These include Condense
>>>>> IUPAC from GMML
>>>>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FGLYCAM-Web%2Fgmml&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=eA9rmh0D7QoyPzvwUBC%2BtIgZxdnQ72QWTx74CWQwpWM%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FGLYCAM-Web%2Fgmml&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=eA9rmh0D7QoyPzvwUBC%2BtIgZxdnQ72QWTx74CWQwpWM%3D&reserved=0>>
> at University
>>>>> of Georgia, WURCS
>>>>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgitlab.com%2Fglyconavi%2Fpdb2glycan&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=TTLXk1QkfdzpSEozxxPuHf58f0EGYjnktH8uNOfoDe0%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgitlab.com%2Fglyconavi%2Fpdb2glycan&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=TTLXk1QkfdzpSEozxxPuHf58f0EGYjnktH8uNOfoDe0%3D&reserved=0>>
> from
>>>>> PDB2Glycan at The Noguchi Institute, Japan, and LINUCS
>>>>> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.glycosciences.de%2Ftools%2Fpdb2linucs%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=dXclDI7KsaKEajEuBxnbxY%2BjshExxyESN2RKDgJdr%2Fo%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.glycosciences.de%2Ftools%2Fpdb2linucs%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=dXclDI7KsaKEajEuBxnbxY%2BjshExxyESN2RKDgJdr%2Fo%3D&reserved=0>>
> from pdb-care at
>>>>> Germany.
>>>>>
>>>>> Furthermore, to ensure continued Findability of 118 common
>>>>> oligosaccharides (e.g., sucrose, Lewis Y antigen), we have expanded the
>>>>> Biologically Interesting molecule Reference Dictionary (BIRD
>>>>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wwpdb.org%2Fdata%2Fbird&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=feM%2F6RPoFqQwdIABus%2BD60JSTSbdi2UzsV62IRKX%2Fvg%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wwpdb.org%2Fdata%2Fbird&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=feM%2F6RPoFqQwdIABus%2BD60JSTSbdi2UzsV62IRKX%2Fvg%3D&reserved=0>>
> ) that contains the covalent linkage
>>>>> information and common synonyms for such molecules.
>>>>>
>>>>> wwPDB has also used this opportunity to improve the organization of
>>>>> chemical synonyms in the CCD by introducing a new
>>>>> _pdbx_chem_comp_synonyms data category. This will enable more
>>>>> comprehensive capture of alternative names for small molecules in the PDB.
>>>>> To minimize disruption to users, the legacy data item,
>>>>> _chem_comp.pdbx_synonyms, will be retained for a transition period
>>>>> through 2021.
>>>>>
>>>>> The carbohydrate remediation project is a wwPDB collaborative project that
>>>>> is carried out principally by RCSB PDB
>>>>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rcsb.org%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=28mQbs4C%2FKygkU5GY1mNYzfX6Y1a76onFlsFwcpsVZU%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rcsb.org%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=28mQbs4C%2FKygkU5GY1mNYzfX6Y1a76onFlsFwcpsVZU%3D&reserved=0>>
> at Rutgers,
>>>>> The State University of New Jersey and is funded by NIGMS grant U01
>>>>> CA221216 in collaboration with Complex Carbohydrate Research Center
>>>>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ccrc.uga.edu%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=gkU8DWkdVXFE%2BCjcV2mEbU6I%2FECM5Dlq2XCErqtQEKk%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ccrc.uga.edu%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=gkU8DWkdVXFE%2BCjcV2mEbU6I%2FECM5Dlq2XCErqtQEKk%3D&reserved=0>>
> at the University of Georgia.
>>>>>
>>>>> If you have any comments or queries regarding the changes to carbohydrate
>>>>> representation, please visit the wwPDB website
>>>>> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wwpdb.org%2Fdocumentation%2Fcarbohydrate-remediation&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6begIrz7OgNq8CecxMhAhm3n%2F4WPAMM%2F4dg9uwmlrcs%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.wwpdb.org%2Fdocumentation%2Fcarbohydrate-remediation&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6begIrz7OgNq8CecxMhAhm3n%2F4WPAMM%2F4dg9uwmlrcs%3D&reserved=0>>
> or
>>>>> contact us at deposit-h...@mail.wwpdb.org <mailto:deposit-
>>>>> h...@mail.wwpdb.org> .
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Regards
>>>>>
>>>>>
>>>>>
>>>>> John
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>>
>>>>> John Berrisford
>>>>>
>>>>> PDBe
>>>>>
>>>>> European Bioinformatics Institute (EMBL-EBI)
>>>>>
>>>>> European Molecular Biology Laboratory
>>>>>
>>>>> Wellcome Trust Genome Campus
>>>>>
>>>>> Hinxton
>>>>>
>>>>> Cambridge CB10 1SD UK
>>>>>
>>>>> Tel: +44 1223 492529
>>>>>
>>>>>
>>>>>
>>>>> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.pdbe.org%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=jtQQunJvDpFvpPIo3b%2BgX0ETtF5TeAvPE07SMtoClQs%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.pdbe.org%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=jtQQunJvDpFvpPIo3b%2BgX0ETtF5TeAvPE07SMtoClQs%3D&reserved=0>
> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.pdbe.org%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=jtQQunJvDpFvpPIo3b%2BgX0ETtF5TeAvPE07SMtoClQs%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.pdbe.org%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=jtQQunJvDpFvpPIo3b%2BgX0ETtF5TeAvPE07SMtoClQs%3D&reserved=0>>
>>>>>
>>>>> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.facebook.com%2Fproteindatabank&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=bPsYJQXaFV05F%2FeeVBASaECt2h13U4HJVNzrfLs2w5k%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.facebook.com%2Fproteindatabank&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=bPsYJQXaFV05F%2FeeVBASaECt2h13U4HJVNzrfLs2w5k%3D&reserved=0>
>>>>> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.facebook.com%2Fproteindatabank&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=bPsYJQXaFV05F%2FeeVBASaECt2h13U4HJVNzrfLs2w5k%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.facebook.com%2Fproteindatabank&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637426199684273018%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=bPsYJQXaFV05F%2FeeVBASaECt2h13U4HJVNzrfLs2w5k%3D&reserved=0>>
>>>>>
>>>>> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftwitter.com%2FPDBeurope&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=mphXsd3vaMR3wlOQ7%2F7p%2FaI3MKG3LPCGSyfVNg%2FCwrg%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftwitter.com%2FPDBeurope&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=mphXsd3vaMR3wlOQ7%2F7p%2FaI3MKG3LPCGSyfVNg%2FCwrg%3D&reserved=0>
> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftwitter.com%2FPDBeurope&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=mphXsd3vaMR3wlOQ7%2F7p%2FaI3MKG3LPCGSyfVNg%2FCwrg%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftwitter.com%2FPDBeurope&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=mphXsd3vaMR3wlOQ7%2F7p%2FaI3MKG3LPCGSyfVNg%2FCwrg%3D&reserved=0>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ________________________________
>>>>>
>>>>> To unsubscribe from the CCP4BB list, click the following link:
>>>>> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=stAI21mrmOvHtv0R5FcepDeFB8CRDK%2FkbPbf8Ffk3Wo%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=stAI21mrmOvHtv0R5FcepDeFB8CRDK%2FkbPbf8Ffk3Wo%3D&reserved=0>
>>>>>
>>>>>
>>>>> ________________________________
>>>>>
>>>>> To unsubscribe from the CCP4BB list, click the following link:
>>>>> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=stAI21mrmOvHtv0R5FcepDeFB8CRDK%2FkbPbf8Ffk3Wo%3D&reserved=0
> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=stAI21mrmOvHtv0R5FcepDeFB8CRDK%2FkbPbf8Ffk3Wo%3D&reserved=0>
>>>>
>>>>
>>>> ########################################################################
>>>>
>>>> To unsubscribe from the CCP4BB list, click the following link:
>>>> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C1%7C637426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=stAI21mrmOvHtv0R5FcepDeFB8CRDK%2FkbPbf8Ffk3Wo%3D&reserved=0
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>>>>
>>>> This message was issued to members of
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> <https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=04%7C01%7Cluca.jovine%40KI.SE%7C1d790a0717ce4217c7a308d897c01b47%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C637426199684282976%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=I7zvQYDZlGewc%2BKWOIDt%2FlPZmV%2Fsscc0hydSQDXOqxU%3D&reserved=0>
>>>
>>>
>>>
>>> När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI
>>> kommer att behandla dina personuppgifter. Här finns information om hur KI
>>> behandlar personuppgifter<https://ki.se/medarbetare/integritetsskyddspolicy
> <https://ki.se/medarbetare/integritetsskyddspolicy>>.
>>>
>>>
>>> Sending email to Karolinska Institutet (KI) will result in KI processing
>>> your personal data. You can read more about KI’s processing of personal
>>> data here<https://ki.se/en/staff/data-protection-policy
> <https://ki.se/en/staff/data-protection-policy>>.
>>>
>>> ########################################################################
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1>
>>>
>>> This message was issued to members of
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>>> <http://www.jiscmail.ac.uk/CCP4BB>, a mailing
> list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>
> <http://www.jiscmail.ac.uk>, terms &
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> <https://www.jiscmail.ac.uk/policyandsecurity/>
>>
>> ########################################################################
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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> <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<http://www.jiscmail.ac.uk/CCP4BB>
>> <http://www.jiscmail.ac.uk/CCP4BB>, a mailing
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> <http://www.jiscmail.ac.uk>, terms &
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>>
>
> ------------------------------------------------------------------------
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> To unsubscribe from the CCP4BB list, click the following link:
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