>Date: Mon, 30 Mar 2009 12:01:10 -0500 >To: Forum for the Proteopedia User Community > <[email protected]> >From: Eric Martz <[email protected]> > >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. >> >> >> >>/* - - - - - - - - - - - - - - - - - - - - - - - - - - - >>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 >>- - - - - - - - - - - - - - - - - - - - - - - - - - - */ >> >> >>_______________________________________________ >>Proteopedialist-for-users mailing list >>[email protected] >>http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users
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