On 02/01/15 23:03, Dale Tronrud wrote:
Happy New Year,
And to you.
I have been comparing the two PDB entries 2EWD and 4ND2 to try to
figure out why the older was replaced by the latter. This task is
surprising hard with Coot, but that is not my issue.
How did you find out why the older was replaced by the latter? (If
indeed you did.)
When I SSM superimposed the A chain from each model a potion of the
text printed to the terminal was confusing. (sorry but I can't figure
out how to cut from a DOS window so I've attached a screen shot.) You
will note that residue 208 matches 208 and 209 matches 209 but then
209 matches 209 again and then 210 matches 209 and then again 210
matches 209. The answer to this riddle is that on the left there
really should be 209A, 209B, 210A, and 210B while on the right it
should be 209 A through D and 210A and 210B. The SSM code is not
writing the insertion codes to the output.
Thanks. Fixed in 0.8.2-pre rev 5485.
A second issue becomes apparent when I open the "Go To Atom..."
dialog box and select 2ewd!A|209A. All four 209 residues are properly
shown in the residue table. The atom table, however shows the atoms
for all four 209 residues. This table is identical when each of the
209 residues are selected. If I select 209A and double-click on the
fourth CA atom I am, indeed, taken to 209D.
Thanks (that bug/oversight has been there since 2004).
Fixed in rev 5486.
Paul.
