The question has to do with SHEET records in .pdb files.
The file 1F88.pdb has some SHEET structures of length 2. That is, they
start at one residue and end at the next.
This is causing a bit of a problem with some of the graphics rendering,
and I need some advice about what to do.
First a little more background.
The code for cartoon/schematic needs to calculate an 'axis' for secondary
structures. For a SHEET, the current sortcut I am taking is as follows:
axisPointA =
midpoint of the alpha carbon atoms of SHEET groups 1 and 2
axisPointB =
midpoint of the alpha carbon atoms of SHEET groups n-1 and n.
Beta sheets have a corrugated/zig-zag pattern. This defines the axis of
the sheet to be between the peaks and troughs. (My plan is to replace this
simple calculation with a 3D least-squares fit.)
However, this does not work when there are only two atoms in the sheet.
Q: In the case where there are only two atoms in a SHEET, should the axis
of the sheet run directly from one alpha carbon to the other?
Any other thoughts/suggestions?
Miguel
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