You can also color by secondary structure by using the following commands:

color purple
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.


Camille wrote:
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 into loop.

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 publication.

Many thanks,