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I would like to download all the PDB files which have crystal structure information in them. But the query builder seems to require me to enter the PDB IDs manually.

Is there a way to get a list of those PDB IDs at RCSB PDB?

Thanks in advance.

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  • $\begingroup$ Thank you for the links. Very useful indeed! $\endgroup$ Jan 28, 2022 at 16:49

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Comment migrated as answer as it inadvertently may have been an answer.

If the sole records in a PDB file that are of interest are EXPDTA,CRYST1 ORIGX1``,ORIGX2, ORIGX3,SCALE1,SCALE2,SCALE3, the in the FTP site the file ftp.wwpdb.org/pub/pdb/derived_data/index/crystal.idx contains this information in a tabular format.

If an extra piece of metadata is sought, such as some of the refinement details in REMARK lines, then the PDBe API can help. In particular, the experiment entrypoint (example) is of interest.

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running the query builder at RCS PDB against id with space group (so crystal info) I get:

172456 hits

more about RCSB PDB web services here: https://www.rcsb.org/docs/programmatic-access/web-services-overview

and the search API here: https://search.rcsb.org/index.html#search-api think you should query for entries where symmetry.pdbx_full_space_group_name_H_M exists (https://search.rcsb.org/structure-search-attributes.html and ask to have returned entry.id (a list of in this case)

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