pdb-l: Chain order changes: a problem for Proteopedia

Eric Martz emartz at microbio.umass.edu
Sun Mar 29 19:27:12 PDT 2009

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".


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)?


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

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