>Date: Sun, 29 Mar 2009 21:27:12 -0500 >To: [email protected], [email protected] >From: Eric Martz <[email protected]> >Subject: Chain order changes: a problem for Proteopedia > >Dear wwPDB: > >The March 17, 2009 remediation of PDB data in the wwPDB (PDB format >3.20) appears to me to have, in many cases, changed the order of >chains, and hence the atom serial numbers in the PDB files. This has >created a major problem in the wiki Proteopedia.Org, where many >molecular scenes that took hours or weeks to develop are now nonfunctional. > >The problem arises becaused Jmol uses atom serial numbers for >selecting groups of atoms when it saves a molecular scene (in a >"state script"). Proteopedia's Scene Authoring Tool uses Jmol's >state scripts to capture molecular scenes and attach them to "green links". > >Questions: > >1. Were the names of ATOM chains ever changed? I assume (and hope) >not, but I have not checked carefully. I see that the chain names >assigned to HETATMs were changed in some cases, e.g. 1e3m, where an >ADP single-residue "chain" originally named chain C (before the 2007 >remediation) is now deemed to be part of chain A (and its position >was moved to the end of the file, after all ATOM records). Since I >have been unable to get pre-March-17 snapshot PDB files (the >snapshot.wwpdb.org server is unresponsive) I am not sure when each >of these changes were made. > >2. Was the changing of chain orders in the March 17 remediation >intentional? If so, is the new order specified somewhere in the 3.20 >documentation? I can see no pattern to the new chain orders (see >examples below). > >3. Were chain orders ever changed in files that contain only protein >chains (no nucleic acids)? > >4. Will the changes in chain order be retained permanently >(requiring substantial repairs to Proteopedia.Org)? > >Observations: > >We first noticed the broken molecular scenes in Proteopedia in cases >that involved DNA. Therefore I have so far limited my inspection of >PDB files to those containing both protein and DNA. > >Since the snapshot ftp server is unresponsive today, my comparisons >were all made between files I had saved before the 2007 remediation >(typically saved 2001-2004), and current files. We have reason to >suspect that changes in chain ordering occurred in the March 17, >2009 remediation, but I cannot verify this for the cases below. > >Some files have NO CHANGE in chain order: > 1d66: DE (DNA), AB (protein). > 1osl: (an NMR multiple model file) AB (protein), CD (DNA). > 1e3m: old AB (protein), C (single residue ADP HETATM "chain"), EF > (DNA); new AB, EF. (ADP now in chain A at the end, thus changing > ATOM serial numbers.) > Thus there appears to be no requirement for nucleic acid or > protein chains to come first. > >Some files that had protein first were rearranged to put DNA first: > 1aoi: old ABCDEFGH (protein), IJ (DNA); new IJ, ABCDEDFH. > 1fzp: old DB (protein), WK (DNA); new WK, DB. > 1hcr: old A (protein), BC (DNA); new BC, A. > Thus there appears to be no requirement that chains be in > alphabetic order. > >One file had an RNA chain moved to BETWEEN two DNA chains, leaving >protein before DNA: > 1qln: old A (protein), TN (DNA), R (RNA); new A (protein), N > (DNA), R (RNA), T (DNA). > The new order happens to be alphabetical by chain name, but > this is not true in other files (see above). > >I did not happen to come across a case where DNA chains preceded >protein in the old format, with protein being moved before DNA in >the new format. > >There also appears to be no requirement that chains be in the order >given in the COMPND records. Examples where the order differs in the >new files: 1flo, 1qln. > >Sincerely, -Eric > >/* - - - - - - - - - - - - - - - - - - - - - - - - - - - >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 >- - - - - - - - - - - - - - - - - - - - - - - - - - - */
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