[Proteopedia] Getting unremediated PDB files: NOW WORKING

[Eric Martz]

Today I am able to get older "snapshot" versions of PDB files. They 
have changed the compression from unix .Z to gzip .gz. So to get 1lbg 
from March 16:

ftp://snapshots.wwpdb.org/20090316/pub/pdb/data/structures/all/pdb/pdb1lbg.ent.gz

To see the list of snapshot dates:

ftp://snapshots.wwpdb.org/

There is a snapshot for January of each year 2005-2009, plus one 
before each of the two remediations, 20070731 and 20090316.

The 20090316 (most recent) snapshot appears to be available.
However, I still get nothing from the 20070731 snapshot.

Regarding the corrupted scene in Proteopedia's Lac Repressor page 
that uses 1lbg (the initial scene in the section "Structure of the 
Lac Repressor"), the order of chains is:
   Before March 17: ABCD (protein), EFGH (DNA).
   After March 17:  EFGH (DNA), ABCD (protein).
Thus, all the atom serial numbers changed, explaining the corruption 
of the scene.

The other scenes on the Lac Repressor page used uploaded PDB files, 
and hence they remain intact.

-Eric

At 3/29/09, Eric Martz wrote:
>In the past, unremediated PDB files could be obtained from 
>ftp://ftp.rcsb.org, however it is stated at http://www.wwpdb.org 
>that this is no longer supported. (This explains why my convenience page
>http://proteinexplorer.org/unremed.htm no longer works.)
>
>Instead, they offer ftp://snapshots.wwpdb.org. However, that URL is 
>not responding today with data. You can get into the folders, but I 
>have not succeeded in retrieving data. There are folders before last 
>year's remediation (20070731) and this year's (20090316). For 
>example, for 1d66.pdb, I have tried
>
>ftp://snapshots.wwpdb.org/20090316/pub/pdb/data/structures/all/pdb/pdb1d66.ent
>
>or
>
>ftp://snapshots.wwpdb.org/20090316/pub/pdb/data/structures/all/pdb/pdb1d66.ent.Z
>
>but I get no response.
>
>
>
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>Eric Martz, Professor Emeritus, Dept Microbiology
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/* - - - - - - - - - - - - - - - - - - - - - - - - - - -
Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst -- http://Martz.MolviZ.Org

Top Five 3D MolVis Technologies http://Top5.MolviZ.Org
3D Wiki with Scene-Authoring Tools http://Proteopedia.Org
Biochem 3D Education Resources http://MolviZ.org
See 3D Molecules, Install Nothing! - http://firstglance.jmol.org
ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il
Atlas of Macromolecules: http://atlas.molviz.org
Workshops: http://workshops.molviz.org
World Index of Molecular Visualization Resources: http://molvisindex.org
PDB Lite Macromolecule Finder: http://pdblite.org
Molecular Visualization EMail List (molvis-list): http://list.molviz.org
Protein Explorer - 3D Visualization: http://proteinexplorer.org
- - - - - - - - - - - - - - - - - - - - - - - - - - - */