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.
|