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 displa
On 13:24 Sat 07 Feb , Paul Emsley wrote:
> hari jayaram wrote:
> Are the residues in helical secondary structure? (the DSSP algorithm is
> built in to Coot - perhaps Pymol uses something else to define ss?)
PyMol indeed has its own algorithm. Here is a brief paste from it:
./layer3/Selector
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
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
Dear Hari --
Not being an expert, I can't answer for you... but it might be a good
idea to post at:
pymol-us...@lists.sourceforge.net
Good luck.
-- Leo --
On 6 Feb 2009, at 17:50, hari jayaram wrote:
I have a low-ish resolution (3.5 ) map for a membrane protein. I
have been using helical
