Dear Rajesh
This is possible with our search API See: http://www.ebi.ac.uk/pdbe/api/doc/search.html For example https://www.ebi.ac.uk/pdbe/search/pdb/select?q=pfam_name:Lipocalin <https://www.ebi.ac.uk/pdbe/search/pdb/select?q=pfam_name:Lipocalin&wt=json> &wt=json then for each result you will need to compare “number_of_polymer_residues” and “max_observed_residues”. This will give you the observed ratio for each molecule (results are per molecule, not per PDB entry) in your result. To make your query you can use our standard search page (pdbe.org) and with a small amount of reformatting use the same query in our search API. For example: If you did a search on a main page the URL would look something like this: https://www.ebi.ac.uk/pdbe/entry/search/index?text:hemoglobin <https://www.ebi.ac.uk/pdbe/entry/search/index?text:hemoglobin&molecule_name:%22Neural%20hemoglobin%22&assembly_composition:%22protein%20structure%22&molecule_type:Protein> &molecule_name:%22Neural%20hemoglobin%22&assembly_composition:%22protein%20structure%22&molecule_type:Protein with all the search parameters encoded in the URL. To use this in the API – take the part after the ? and change & to “ AND “ – the spaces are important here. i.e. text:hemoglobin&molecule_name:"Neural%20hemoglobin"&assembly_composition:"protein%20structure"&molecule_type:Protein becomes text:haemoglobin AND molecule_name:"Neural%20hemoglobin" AND assembly_composition:"protein%20structure" AND molecule_type:Protein then append this to our search API URL (https://www.ebi.ac.uk/pdbe/search/pdb/select?q=) https://www.ebi.ac.uk/pdbe/search/pdb/select?q=text:hemoglobin AND molecule_name:"Neural%20hemoglobin" AND assembly_composition:"protein%20structure" AND molecule_type:Protein and then if you prefer JSON format to XML add &wt=json to the end. https://www.ebi.ac.uk/pdbe/search/pdb/select?q=text:hemoglobin AND molecule_name:"Neural%20hemoglobin" AND assembly_composition:"protein%20structure" AND molecule_type:Protein&wt=json By default this will get you 10 result – to get more add &rows=10 to the end and change 10 to a larger number. Hope this helps John From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Rajesh Sent: 27 September 2017 23:48 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] PDB search help Dear BB, Sorry for the off topic. Does anyone know how to search the PDB for the entries that have the density only for part of the protein molecule rather than for the entire length of the protein attempted to crystallize? Thanks, Rajesh..
