pdb-l: Chain order changes: a problem for Proteopedia
emartz at microbio.umass.edu
Sun Mar 29 19:27:12 PDT 2009
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
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
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
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
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.
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Eric Martz, Professor Emeritus, Dept Microbiology
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