The last time I looked (which was some time ago!) PyMol would
cartoonize if EITHER (a) the secondary structure was defined in the
PDB file; OR (b) the Action Menu item "assign sec. struc." was
selected. I don't know when this behavior changed, but the latest
build from fink seems to display cartoon renderings independently of
the presence or absence of HELIX and SHEET records.
You might also check the order of the atom records in the peptide
bonds in case an unexpected ordering is confusing PyMol.
Lynn Ten Eyck
On 7 Feb 2009, at 05:24, Paul Emsley wrote:
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.
