RE: [PyMOL] Displaying/defining double bonds in a ligand molecule

[Warren D. <wa...@de...>]

Wulf,

Unfortunately, the lighting model has changed...I am assuming that you =
are having problems with existing session files or scripts? =20

It may be necessary to reoptimize the lighting settings.  The new =
defaults are:

set ambient, 0.14
set gamma, 1.0
set direct, 0.45
set reflect, 0.45
set specular_intensity, 0.5
set light_count, 2=20
set light, [ -0.40000, -0.40000, -1.00000 ]=20
set spec_reflect, -1
set spec_power, -1
set shininess, 55

Perhaps you can simply paste those commands into your scripts?

If you want pre-0.99-like lighting model (it has an extra dot product =
that shouldn't be there).

use=20

set ray_legacy_lighting, 1

with the above settings

Cheers,
Warren

-----Original Message-----
From: Wulf Blankenfeldt [mailto:wul...@mp...]
Sent: Mon 3/6/2006 7:23 AM
To: Warren DeLano
Subject: Re: [PyMOL] Displaying/defining double bonds in a ligand =
molecule
=20
Ah, bingo!

Thanks for that, Warren.


BTW: we have a little difficulty with the 0.99 version under windows:=20
colours have become very glary in raytracing, like an overexposed=20
photograph. Is this a feature, a non-optimised colour scheme or simply=20
my mistake?


Best,



Wulf




Warren DeLano schrieb:
>
> Wulf,
>
> The easiest thing would be to convert your small molecule to an SDF,=20
> MOL, or MOL2 format before loading it into PyMOL.
>
> Short of that, you'd have to select each bond independently=20
> (ctrl-right-click while in editing mode) and use Ctrl-W to set the=20
> valences.
>