[PyMOL] rendering missing segments

[Seth H. <se...@gm...>]

Hi Thomas et al,

There was a recent question on the board about missing residues and the
possibility of reading SEQRES headers and PyMOL being able to show the
missing bits in the sequence view, perhaps with the amino acid letters
grayed out to distinguish the gap. I know the reply was "PyMOL doesn't
currently" do this, but it seemed to then end "full stop" rather than,
"...but it's a fantastic idea". I'd like to second the idea as a great
addition! When building structures or viewing and hitting gaps one always
has to shuffle off to find the sequence or jump back to see how big the gap
is and what type of residues are supposed to be in there. This would put it
right there integrated at one's fingertips.

This also reminds me of something I suggested to you, Thomas, that might
fit in here of having a "cartoon dash" rendering (at least for loops if not
helices and strands?) such that one could borrow a loop from a homologue or
build in a placeholder to provide visual continuity in a model while still
clearly indicating the disordered regions, but now in a 3D ray-traced
dashed line that follows the cartoon trajectory rather than the usual
penciled in job.

I know in building a new structure I don't often have any SEQRES header in
place, but if it offered advantages like this it would be easy enough to
install such.

Thanks,
Seth