Re: [PyMOL] Display style for partial bond

[Thomas H. <tho...@sc...>]

Hi Martin,

only distance measures can draw dashed lines in PyMOL, so try this:

unbond elem W, elem C
show sticks
show sphere, elem W
distance transbonds, elem W, elem C
hide label
set dash_round_ends, off
set dash_radius, 0.2
set dash_length, 0.4
set dash_gap, 0.15
ray

The dashes will display as nice cylinders when ray traced and also with
the new shader rendering in PyMOL 1.5 (set use_shaders).

Cheers,
  Thomas

Martin Hediger wrote, On 02/26/13 09:57:
> Dear PyMOL Users
> 
> If you load these coordinates in PyMOL
> 
> HETATM    1  W   LIG     1      -1.357  -0.079   0.052  1.00  0.00           W
> HETATM    2  C   LIG     1      -0.713  -1.686   1.008  1.00  0.00           C
> HETATM    3  C   LIG     1      -0.323  -1.855  -0.270  1.00  0.00           C
> HETATM    4  H   LIG     1      -0.664  -2.180   1.970  1.00  0.00           H
> HETATM    5  H   LIG     1      -0.441  -2.597  -1.043  1.00  0.00           H
> 
> you'll see that a bond between W and C is drawn. However, this is 
> supposed to be a transition state, so a dashed bond would be more 
> appropriate. Can this somehow be drawn?
> 
> Thanks,
> Martin

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor