>Date: Sun, 29 Mar 2009 21:21:35 -0500 >To: [email protected] >From: Eric Martz <[email protected]> >Subject: Atom serial numbers vs. Jmol/Proteopedia >Cc: [email protected], [email protected], >[email protected] > >It appears to me that one source of major problems with existing >scenes in Proteopedia, vs. the March 17 remediation of the wwPDB >(PDB format 3.20), concerns atom serial numbers that changed. Jmol's >state scripts (used to save scenes in Proteopedia) use atom serial >numbers extensively in select commands. The re-ordering of serial >numbers in the 3.20 remediation causes the wrong atoms to be >selected in Proteopedia scenes. > >An example is some scenes of the nucleosome, >http://proteopedia.org/wiki/index.php/User:Eric_Martz/Nucleosomes > >Here, five of six green links now produce seriously damaged scenes. > >The order of chains was changed in 3.20. In a 2005 version of >1aoi.pdb that I have (which also antedates the August 1, 2007 >remediation), protein chains are first, followed by DNA: atom serial >1 is in protein chain A. In the current version, DNA is first: atom >serial 1 is in DNA chain I. Thus, scripts that depend on serial >numbers will produce scrambled results. If this problem is limited >to PDB files containing nucleic acids, this would explain our >impression that mostly scenes with DNA are damaged. I have not >checked multiple chain protein-only files. >Old 1aoi chain order: ABCDEFGH IJ. >New 1aoi chain order: IJ ABCDEFGH. > >I examined a few other cases where I happen to have old versions of >PDB files, since the snapshots ftp server appears to be down today. >The results are organized more systematically in a separate message >I am sending to the pdb-l. > > - 1lbg (used in the damaged scene in the Lac Repressor page) I do > not have an old copy of this file. > > - 1osl (NMR multi model file). Order of chains is protein, then > DNA -- both before Mar 17, and currently. So here, unlike with > 1aoi, the DNA was not put before the protein. > > - 1d66. In my 2006 copy, the first chain is DNA chain D, followed > by another DNA chain E, and 2 protein chains A and B. This order is > not changed in the current version. Both files end protein with >ATOM 1710 CD2 LEU B 64 > > - 1fzp (My copy is from 2001.) Old version has protein chains D, B > followed by DNA chains W, K. Current version has chain order > reversed (WKDB), so different atom serial numbers. > > - 1hcr (My copy is from 2001.) Old version has protein chain A > followed by DNA chains B, C. Current version has chain order > reversed (B, C, A), so different atom serial numbers. > > - 1qln (My copy is from 2002.) Both old and current versions have > chain order protein, nucleic. However, the order of chains is > changed. Old: chains A, T, N, R. A is protein, T and N are DNA, and > R is RNA. The last atom in the old file is "ATOM 7508 C4 G > R 3". The order in the current file is A, N, R, T, which differs > from the order given in the COMPND records. The last atom in the > current file is "ATOM 7508 C4 DA T 22". Thus, the serial > numbers are changed. > > - 1flo (My copy is from 2004.) Old file has 4 protein chains > followed by 8 DNA chains, ABCD, EGIK, FGHL. In the new file, the > order is EFGHIJKL, ABCD. The DNA chain order for ATOM records > differs from the order in the COMPND records. Thus the serial > numbers are changed. > > - 1e3m (My copy is from 2002.) Old file has protein chains A, B, > then HETATM chain C (a single residue ADP "chain"), then DNA chains > E, F. The new file has the same order of true chains A, B, E, F, > followed by ADP deemed to be part of chain A. Thus, some serial > numbers are changed. The last atom in chain F is (old file) > "ATOM 12915 C6 T F 30", and (new file) "ATOM 12888 C7 DT F 30". > > >At http://www.wwpdb.org in the 3.20 documentation I did not find any >specification for the order of chains, but I may well have missed it. > >It may be worth suggesting a change in Jmol to avoid using atom >serial numbers in state scripts, in case a future remediation again >scrambles the serial numbers. > >In my separate message to the PDB, I am asking whether the changes >in chain order were intentional, what the specification for chain >order is (it is not obvious to me), and whether these changes will >be permanent (requiring repairs in Proteopedia). > >-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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