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

Eric Martz emartz at microbio.umass.edu
Sun Mar 29 22:28:20 EDT 2009

>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".
>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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