hari jayaram wrote:
I have a low-ish resolution (3.5 ) map for a membrane protein. I have
been using helical restraints heavily in pymol to do the model building
(versions 0.4.2 to 0.5.1 to 0.6 pre release ) . The structure is very
homologous to something else and these are really long membrane spanning
helices. So a large part of the structure should be helical and thats
my justification for using the restraints in coot.
I have mostly refined in refmac ( newest 5.3 ) and some in phenix. Both
of these pick the refining restraints automagically.
My problem is that my helices look perfect in coot , with the torsions
and h-bonding looking pretty good .All the traffic lights ( with and
without torsional and ramchandran and helical restraints) are green. But
pymol simply refuses to cartoonize my "helices" as helix.
I know I can force the pymol cartoon algorithm to treat those regions as
helix but am concerned that something is not correct in the way I built
my model.
Any clues on forcing my helices to conform to what pymols idea of a
helix is. The pymol version is also 1.0r2 and does cartoonize everything
else as expected.
Are the residues in helical secondary structure? (the DSSP algorithm is
built in to Coot - perhaps Pymol uses something else to define ss?)
You can look at the sequence view (coloured by secondary structure) or
view as CA with Secondary Structure to see if Coot (at least) thinks
your residues are alpha helices.
Paul.
