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[Jmol-users] Fwd: Re: Chain order changes: a problem for Proteopedia
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From: Eric M. <em...@mi...> - 2009-03-30 21:16:32
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<html> <body> Dear Bob,<br><br> How difficult would it be to change the state script generator in Jmol to avoid using atom serial numbers?<br><br> I'm sure none of us ever envisioned the current state of affairs. We have who knows how many state scripts saved in Proteopedia, and now an unknown number of March-17-remediated PDB files have scrambled atom serial numbers. Further, there is no guarantee that such scrambling will not occur again in a future remediation.<br><br> A change in Jmol to avoid serial number dependency in saved state scripts will not avoid the need for repairs to Proteopedia now, but may avoid such calamities in the future.<br><br> Regards, -Eric<br><br> <blockquote type=cite class=cite cite="">Date: Mon, 30 Mar 2009 15:09:56 -0400<br> From: John Westbrook <jw...@rc...><br> Reply-To: jw...@rc...<br> Organization: RCSB - Protein Data Bank<br> To: em...@mi...<br> CC: Helen Berman <be...@rc...>, Kim Henrick <he...@eb...><br> Subject: Re: Chain order changes: a problem for Proteopedia <br><br> Dear Eric,<br><br> In producing the V3.2 wwPDB release, we have tried to preserve as much<br> as possible the PDB chain and residue nomenclature for polymer molecular components.<br> With version 3.2 comes the introduction of more uniform assignment<br> PDB chain identifiers for ligands and solvent, so this has resulted in<br> some nomenclature changes in V3.2 files.<br><br> <font color="#FF0000">Neither the V2.6 nor V3.2 format specifications suggests that the atom serial<br> number be used as the primary atom identifier.</font> I am sure that you are aware that<br> there are now many PDB entries that have been split across multiple PDB data<br> files specifically because of the limitation in the range atom serial numbers.<br> Atom serial numbers are also replicated between models so they do not represent<br> unique atom identifiers for NMR or other multi-model entries.<br><br> If you have a specific dependency prior atom serial numbers in your software<br> system, then you can always recover the particular version of the PDB entry<br> that you used from our ftp snapshot server (<a href="ftp://snapshots.rcsb.org/" eudora="autourl"> ftp://snapshots.rcsb.org</a>).<br><br> I should point out that we provided Jaim with an advanced copy of the<br> V3.2 files for testing on Dec 3, 2008. The issue of atom ordering<br> was not raised as an issue at that time.<br><br> Regards,<br><br> John<br><br> <br><br> >>><br> >>> Begin forwarded message:<br> >>><br> >>>> From: Eric Martz <em...@mi...><br> >>>> Date: March 29, 2009 7:27:12 PM PDT<br> >>>> To: "in...@rc..." <in...@rc...>, "pd...@rc..." <pd...@rc...><br> >>>> Subject: pdb-l: Chain order changes: a problem for Proteopedia<br> >>>><br> >>>> Dear wwPDB:<br> >>>><br> >>>> The March 17, 2009 remediation of PDB data in the wwPDB (PDB format<br> >>>> 3.20) appears to me to have, in many cases, changed the order of<br> >>>> chains, and hence the atom serial numbers in the PDB files. This has<br> >>>> created a major problem in the wiki Proteopedia.Org, where many<br> >>>> molecular scenes that took hours or weeks to develop are now<br> >>>> nonfunctional.<br> >>>><br> >>>> The problem arises becaused Jmol uses atom serial numbers for<br> >>>> selecting groups of atoms when it saves a molecular scene (in a<br> >>>> "state script"). Proteopedia's Scene Authoring Tool uses Jmol's state<br> >>>> scripts to capture molecular scenes and attach them to "green links".<br> >>>><br> >>>> Questions:<br> >>>><br> >>>> 1. Were the names of ATOM chains ever changed? I assume (and hope)<br> >>>> not, but I have not checked carefully. I see that the chain names<br> >>>> assigned to HETATMs were changed in some cases, e.g. 1e3m, where an<br> >>>> ADP single-residue "chain" originally named chain C (before the 2007<br> >>>> remediation) is now deemed to be part of chain A (and its position<br> >>>> was moved to the end of the file, after all ATOM records). Since I<br> >>>> have been unable to get pre-March-17 snapshot PDB files (the<br> >>>> snapshot.wwpdb.org server is unresponsive) I am not sure when each of<br> >>>> these changes were made.<br> >>>><br> >>>> 2. Was the changing of chain orders in the March 17 remediation<br> >>>> intentional? If so, is the new order specified somewhere in the 3.20<br> >>>> documentation? I can see no pattern to the new chain orders (see<br> >>>> examples below).<br> >>>><br> >>>> 3. Were chain orders ever changed in files that contain only protein<br> >>>> chains (no nucleic acids)?<br> >>>><br> >>>> 4. Will the changes in chain order be retained permanently (requiring<br> >>>> substantial repairs to Proteopedia.Org)?<br> >>>><br> >>>> Observations:<br> >>>><br> >>>> We first noticed the broken molecular scenes in Proteopedia in cases<br> >>>> that involved DNA. Therefore I have so far limited my inspection of<br> >>>> PDB files to those containing both protein and DNA.<br> >>>><br> >>>> Since the snapshot ftp server is unresponsive today, my comparisons<br> >>>> were all made between files I had saved before the 2007 remediation<br> >>>> (typically saved 2001-2004), and current files. We have reason to<br> >>>> suspect that changes in chain ordering occurred in the March 17, 2009<br> >>>> remediation, but I cannot verify this for the cases below.<br> >>>><br> >>>> Some files have NO CHANGE in chain order:<br> >>>> 1d66: DE (DNA), AB (protein).<br> >>>> 1osl: (an NMR multiple model file) AB (protein), CD (DNA).<br> >>>> 1e3m: old AB (protein), C (single residue ADP HETATM "chain"), EF<br> >>>> (DNA); new AB, EF. (ADP now in chain A at the end, thus changing ATOM<br> >>>> serial numbers.)<br> >>>> Thus there appears to be no requirement for nucleic acid or<br> >>>> protein chains to come first.<br> >>>><br> >>>> Some files that had protein first were rearranged to put DNA first:<br> >>>> 1aoi: old ABCDEFGH (protein), IJ (DNA); new IJ, ABCDEDFH.<br> >>>> 1fzp: old DB (protein), WK (DNA); new WK, DB.<br> >>>> 1hcr: old A (protein), BC (DNA); new BC, A.<br> >>>> Thus there appears to be no requirement that chains be in<br> >>>> alphabetic order.<br> >>>><br> >>>> One file had an RNA chain moved to BETWEEN two DNA chains, leaving<br> >>>> protein before DNA:<br> >>>> 1qln: old A (protein), TN (DNA), R (RNA); new A (protein), N<br> >>>> (DNA), R (RNA), T (DNA).<br> >>>> The new order happens to be alphabetical by chain name, but<br> >>>> this is not true in other files (see above).<br> >>>><br> >>>> I did not happen to come across a case where DNA chains preceded<br> >>>> protein in the old format, with protein being moved before DNA in the<br> >>>> new format.<br> >>>><br> >>>> There also appears to be no requirement that chains be in the order<br> >>>> given in the COMPND records. Examples where the order differs in the<br> >>>> new files: 1flo, 1qln.<br> >>>><br> >>>> Sincerely, -Eric<br> >>>><br> >>>> /* - - - - - - - - - - - - - - - - - - - - - - - - - - -<br> >>>> Eric Martz, Professor Emeritus, Dept Microbiology<br> >>>> U Mass, Amherst -- <a href="http://martz.molviz.org/" eudora="autourl"> http://Martz.MolviZ.Org</a><br> >>>><br> >>>> Top Five 3D MolVis Technologies <a href="http://top5.molviz.org/" eudora="autourl"> http://Top5.MolviZ.Org</a><br> >>>> 3D Wiki with Scene-Authoring Tools <a href="http://proteopedia.org/" eudora="autourl"> http://Proteopedia.Org</a><br> >>>> Biochem 3D Education Resources <a href="http://molviz.org/" eudora="autourl">http://MolviZ.org</a><br> >>>> See 3D Molecules, Install Nothing! - <a href="http://firstglance.jmol.org/" eudora="autourl"> http://firstglance.jmol.org</a><br> >>>> ConSurf - Find Conserved Patches in Proteins: <a href="http://consurf.tau.ac.il/" eudora="autourl"> http://consurf.tau.ac.il</a><br> >>>> Atlas of Macromolecules: <a href="http://atlas.molviz.org/" eudora="autourl"> http://atlas.molviz.org</a><br> >>>> Workshops: <a href="http://workshops.molviz.org/" eudora="autourl"> http://workshops.molviz.org</a><br> >>>> World Index of Molecular Visualization Resources:<br> >>>> <a href="http://molvisindex.org/" eudora="autourl"> http://molvisindex.org</a><br> >>>> PDB Lite Macromolecule Finder: <a href="http://pdblite.org/" eudora="autourl">http://pdblite.org</a><br> >>>> Molecular Visualization EMail List (molvis-list):<br> >>>> <a href="http://list.molviz.org/" eudora="autourl"> http://list.molviz.org</a><br> >>>> Protein Explorer - 3D Visualization: <a href="http://proteinexplorer.org/" eudora="autourl"> http://proteinexplorer.org</a><br> >>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - */<br> >>>><br> >>>><br> >>>> TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see<br> >>>> <a href="https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l" eudora="autourl"> https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l</a> .<br> >>><br><br> <br> -- <br> ******************************************************************<br> John Westbrook, Ph.D.<br> Rutgers, The State University of New Jersey<br> Department of Chemistry and Chemical Biology<br> 610 Taylor Road<br> Piscataway, NJ 08854-8087<br> e-mail: jw...@rc...<br> Ph: (732) 445-4290 Fax: (732) 445-4320<br> ******************************************************************</blockquote> </body> </html> |