Rotate axis, angle, object:
rotate [-0.69156,-0.697508,0.1877], 45, FRETSetNew5Down
See tips on this
translate vector [,selection
sort object
Alter selection, expression
Example : Rechain: Alter chain b, chain='c' rechains from b to c
Distance name = selection, selection
Creates a distance object between the selections
Automated measuring of distances, taken from tips
Measure specific distances
from pymol import cmd
f=open('dist.txt','w')
dst=cmd.distance('tmp','mol1///25/ha','mol1///26/ha')
f.write("%8.3f\n"%dst)
f.close()
With looping:
from pymol import cmd
f=open('dist.txt','w')
atom = cmd.get_model("mol1////ha").atom
for i in range(len(atom)-1):
sele1 = 'mol1///%s/HA'%atom[i].resi
sele2 = 'mol1///%s/HA'%atom[i+1].resi
dst=cmd.distance('tmp',sele1,sele2)
f.write("%14s %14s %8.3f\n"%(sele1,sele2,dst))
f.close()
cd directory
changes the default working directory (initiall '~')
Marking atoms (see tips)
Png filename
Write a PNG graphics file of the screen
ray width, height
Save a PovRAY file of the image on the screen
See tips on this
scene F3, store, message
Stores the current view as one of the menu-accessible views
scene anystring, store, message
Stores the current view in script-accessible views
Show ball and stick model:
hide lines
show sticks
show spheres
set stick_radius=0.1
set sphere_scale=0.25