#27 improve flexibility for cartoon segment display

open
nobody
5
2012-12-06
2008-09-25
No

Copied from an email request:

"we were thinking more about no-overlapping
neighboring residues that are defined as strands, e.g. i and i+1, are both
"strand", but they are in two different strands. This is a common
situation is beta-turns. It shows very nicely in MolScript, but PyMol
shows a single strand turning all the way back. The trick is that
one-side of the residue is a loop, and the other one is a turn, so
secondary structure in this case is not a property of a residue, but
property of a residue half"

So we're considering the possibility of allowing the user to specify both forward and backward cartoon segment types for a residue by expanding the cartoon property associated with the control atom.

Currently we support ss = S H or L (equivalent to blank), where all transitions occur at the CA atom position, and there is no such thing as a one-residue segment other than a loop.

Might also consider supporting ss =

SS (sheets extends out an additional half-residue)

HH (helix representation extends out an additional half-residue)

LL (loop representation extends out an additional half-residue)

SH (sheet transitions into helix)

HS (helix transitions into sheet)

S.S (two adjacent discontinuous sheets)

H.H (two adjacent discontinuous helices)

S. (sheet break after residue)

.S (sheet with break before residue)

.S. (sheet breaks on both sides of residue)

same three as above for H / helix?

need to think some more about this...

Discussion