[Proteopedia] Fwd: Chain order changes: a problem for Proteopedia

[Dan Bolser]

Lets hope that the changes are all documented this time. If they were
intentional, at least it should be possible to automatically re-map
selections through the documentation... in theory... the track record
on this issue is not good however.

Dan.

2009/3/30 Eric Martz <emartz at microbio.umass.edu>:
>
>> Date: Sun, 29 Mar 2009 21:27:12 -0500
>> To: info at rcsb.org, pdb-l at rcsb.org
>> From: Eric Martz <emartz at microbio.umass.edu>
>> 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
>>
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