You can also color by secondary structure by using the following
color orange, ss s
color mred2, ss h
The first command colors everything purple, including loops. The second
colors all beta strands orange, and the third colors all helices mred2.
Hello Pymol community,
I'm experiencing a problem when colouring a pdb by secondary
structure. The colour bleeds from the ends of helices and sheets
for example, if I were to....
color orange, a/49:52/
color purple, a/53:55/
color mred2, a/56:59/
where a/49:52/ is beta strand and a/53:55/ is loop and a/56:59/ is
beta strand, I get bleed from the ends of the strand into the loop.
Is there any way around this to get the colors to only apply to the
defined secondary structure elements (I read in an ss_pml with
"alter... yada yada yada....") as in molscript?
I apologise if this question has been dealt with before (I have
tried to find previous messages). I imagine that this would be
important to many who would like to use pymol to make figures for