On Mon, Mar 30, 2009 at 4:16 PM, Eric Martz <[email protected]>wrote:
> Dear Bob,
>
> How difficult would it be to change the state script generator in Jmol to
> avoid using atom serial numbers?
>
impossible. It has to use atom index numbers (what you are calling "serial
numbers"). That I know.
>
> 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.
>
right, so if you are focused on a specific PDB file as with a script, you
will need to make a copy and use it, not go back to the PDB for it. I'm
afraid that's just the situation.
>
> 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.
>
I don't think so. No matter what you do, scripts accessing files they were
not initially intended to access will be prone to difficulties. For example,
some of the new PDB files have new chain lettering. Well, selecting {*:A}
would not work then, regardless of the atom indexing problem. I just don't
see any way around it but for scripts to access copies if they are intended
to have any longevity. It's just good practice -- access a local version,
not somebody else's data.
Bob
>
> Regards, -Eric
>
> Date: Mon, 30 Mar 2009 15:09:56 -0400
> From: John Westbrook <[email protected]>
> Reply-To: [email protected]
> Organization: RCSB - Protein Data Bank
> To: [email protected]
> CC: Helen Berman <[email protected]>, Kim Henrick <[email protected]
> >
> Subject: Re: Chain order changes: a problem for Proteopedia
>
> Dear Eric,
>
> In producing the V3.2 wwPDB release, we have tried to preserve as much
> as possible the PDB chain and residue nomenclature for polymer molecular
> components.
> With version 3.2 comes the introduction of more uniform assignment
> PDB chain identifiers for ligands and solvent, so this has resulted in
> some nomenclature changes in V3.2 files.
>
> Neither the V2.6 nor V3.2 format specifications suggests that the atom
> serial
> number be used as the primary atom identifier. I am sure that you are
> aware that
> there are now many PDB entries that have been split across multiple PDB
> data
> files specifically because of the limitation in the range atom serial
> numbers.
> Atom serial numbers are also replicated between models so they do not
> represent
> unique atom identifiers for NMR or other multi-model entries.
>
> If you have a specific dependency prior atom serial numbers in your
> software
> system, then you can always recover the particular version of the PDB entry
> that you used from our ftp snapshot server ( ftp://snapshots.rcsb.org).
>
> I should point out that we provided Jaim with an advanced copy of the
> V3.2 files for testing on Dec 3, 2008. The issue of atom ordering
> was not raised as an issue at that time.
>
> Regards,
>
> John
>
>
>
> >>>
> >>> Begin forwarded message:
> >>>
> >>>> From: Eric Martz <[email protected]>
> >>>> Date: March 29, 2009 7:27:12 PM PDT
> >>>> To: "[email protected]" <[email protected]>, "[email protected]" <[email protected]
> >
> >>>> Subject: pdb-l: 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 <http://martz.molviz.org/>
> >>>>
> >>>> Top Five 3D MolVis Technologies
> >>>> http://Top5.MolviZ.Org<http://top5.molviz.org/>
> >>>> 3D Wiki with Scene-Authoring Tools
> >>>> http://Proteopedia.Org<http://proteopedia.org/>
> >>>> Biochem 3D Education Resources http://MolviZ.org <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
> >>>> - - - - - - - - - - - - - - - - - - - - - - - - - - - */
> >>>>
> >>>>
> >>>> TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see
> >>>> https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l .
> >>>
>
>
> --
> ******************************************************************
> John Westbrook, Ph.D.
> Rutgers, The State University of New Jersey
> Department of Chemistry and Chemical Biology
> 610 Taylor Road
> Piscataway, NJ 08854-8087
> e-mail: [email protected]
> Ph: (732) 445-4290 Fax: (732) 445-4320
> ******************************************************************
>
>
>
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