SCOPe Funding Alert: SCOPe support from the NIH ended in April 2016. John-Marc Chandonia is the primary maintainer and has continued to develop SCOPe using vacation time. Three proposals to the NIH for continued funding have been unsuccessful. If our current NIH proposal is not funded, SCOPe will shut down permanently in Summer 2017 as Dr. Chandonia will need to seek a new position.

PDB-style files for SCOPe domains

The ATOM and HETATM records corresponding to each SCOPe domain have been collated into PDB-style coordinate files. Header and remark records with more information about the domain are also provided.

Access:

  • The archive of all PDB-style files has been split into 6 parts because the file size exceeds 2 GB. To get all the PDB-style files for Astral 2.06, download part 1 (1.5 GB), part 2 (1.5 GB), part 3 (1.6 GB), part 4 (1.6 GB), part 5 (1.5 GB) and part 6 (1.7 GB). Parts 1 - 5 contain files in which the data (excluding the REMARK comments) have not changed since 2.05. Part 6 contains files in which the data and REMARK comments have both changed. All files will unpack into a single directory.
    Bug fix: If you downloaded the files before 4 May 2016, part 7 (5.7 MB) contains files with correct coordinates for 9,166 expression tag domains that were incorrectly generated (mostly single-residue domains, along with some of the tags that included negative residue identifiers); if you download the files after 4 May, you don't need this, since the fixes are integrated into part 6 above.

  • If you only need smaller subsets of these files, you can instead download archives containing the PDB-style files corresponding to our two most commonly requested genetic domain sequence subsets: the 40% ID filtered subset (937.1 MB) and the 95% ID filtered subset (1.9 GB).

  • If you have a set of older PDB-style files, you may want to download only those files in which the data have changed. A list showing the last Astral version in which the data (not headers) in each PDB-style file was last updated is here: pdbstyle-updated-2.06.txt

  • For direct access to all the files, click here.

  • or use this form to retrieve the file for a single domain by either the SCOPe sid or sun identifiers:
    the PDB-style file for SCOPe domain (i.e. "d1dlwa_" or "14982")
    Output will be returned as .

Notes:

  • Domains in the file hierarchy are named according to SCOPe sid ID, not Astral ID, in cases where they are different (multi-chain domains begin with "g" or "e" in Astral and "d" in SCOPe). Either ID will work in the above form, as well as the numeric sun IDs from SCOPe.

  • For domains containing multiple chains, the chains are ordered in the genetic domain order (as is the case for the sequences), not the order in the original PDB file. For example, chain B: may appear before chain A:

  • For entries containing multiple models, all models are included, along with MODEL and ENDMDL records.

  • We have inserted a TER record for each chain, and an END record at the end of the file.

  • The header and remark records take the following form:
    HEADER    SCOPe/ASTRAL domain d1dlwa_ [14982]      28-JUL-05   0000
    REMARK  99
    REMARK  99 ASTRAL ASTRAL-version: 1.75
    REMARK  99 ASTRAL SCOPe-sid: d1dlwa_
    REMARK  99 ASTRAL SCOPe-sun: 14982
    REMARK  99 ASTRAL SCOPe-sccs: a.1.1.1
    REMARK  99 ASTRAL Source-PDB: 1dlw
    REMARK  99 ASTRAL Source-PDB-REVDAT: 20-SEP-00
    REMARK  99 ASTRAL Region: a:
    REMARK  99 ASTRAL ASTRAL-SPACI: 0.66
    REMARK  99 ASTRAL ASTRAL-AEROSPACI: 0.66
    REMARK  99 ASTRAL Data-updated-release: 1.61