DSSP did indeed think they were helices. Also thanks for the sec str coloring tip-didnt realize coot had that feature. For the model coot also colors the helices pink as would be expected.
So it must be that pymol cartoons still dont implement "DSSP" ..which I thought was the case Hari On Sat, Feb 7, 2009 at 8:24 AM, Paul Emsley <paul.ems...@bioch.ox.ac.uk>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. >
