Search for specific PDB chain

Jalview Developers
1

Dear Swanand,

I am wondering if there is a way to query for a specific PDB chain via the PDB Search API?

Having the ability to do this would really be helpful, especially for cases where a PDB entry has several chains (i.e. 4v88 - 162 chains), and the user already has a specific chain he intends to retrieve.

Please kindly advise where to look if this functionality already exists.

Thanks and regards,
Charles

Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
College of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk​

The University of Dundee is a registered Scottish Charity, No: SC015096

2

Dear Swanand,

Thanks for the prompt reply. Ideally we want to be able to get all the information available in the PDB polymeric entity, in addition to the domain mappings for a specific PDB chain. However, the first problem is how to identify the various chains available. At the moment, the PDB API provides information about the number of chains available but does give any other information about them.

Hence, I suggest the introduction of a new array field ( say chain_ids) to capture the Ids for all the available chains for each entry. For instance, 4yms has the following four chains: A, D, C and J hence the retrieved PDB doc for it should contain the data chain_ids:[‘A’,’D’,’C’,J]. Subsequently, a chain code could then be pick and queried together with the main PDB Id to get the domain mapping for that particular chain.

Best regards,
Charles

Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
College of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk​

···

Dear Charles,

Yes I agree with you in general, that it’s useful to get information on a single chain instead of all chains in an entry. Are you thinking of situations where you want validation information or domain mappings for only one of the chains, but instead have to make a call that returns those for all chains? We are creating equivalent chain-wise calls e.g. for entry/residue_listing. If you have any particular calls in mind, please let us know and we could expedite their release.

Thanks and regards,
Swanand

-- 
Swanand Gore, wwPDB at PDBe-EMBL-EBI, Cambridge
[swanand@ebi.ac.uk](mailto:swanand@ebi.ac.uk) ............. [http://pdbe.org](http://pdbe.org/)
3

Dear Swanand,

Sorry to bother you, I was wondering if you have any update regarding the issue raised in the email below?

A feedback would be highly appreciated as a couple of features we are planing to implement in Jalview depends on this, and we want to know where to go from here as soon as possible.

Thanks and regards,
Charles

Ofoegbu Tochukwu Charles
Jalview Visual Analytics Developer/Scientist
The Barton Group
Division of Computational Biology
College of Life Sciences
University of Dundee, Dundee, Scotland, UK.
Skype: cofoegbu
www.jalview.org
www.compbio.dundee.ac.uk​

···

Dear Charles,

Yes I agree with you in general, that it’s useful to get information on a single chain instead of all chains in an entry. Are you thinking of situations where you want validation information or domain mappings for only one of the chains, but instead have to make a call that returns those for all chains? We are creating equivalent chain-wise calls e.g. for entry/residue_listing. If you have any particular calls in mind, please let us know and we could expedite their release.

Thanks and regards,
Swanand

-- 
Swanand Gore, wwPDB at PDBe-EMBL-EBI, Cambridge
[swanand@ebi.ac.uk](mailto:swanand@ebi.ac.uk) ............. [http://pdbe.org](http://pdbe.org/)