RE: [PyMOL] Fancy images

[DeLano, W. <wa...@su...>]

Robert,

   You are on the right track.  In order to do this right, you'll need =
to use PovRay, which supports perspective and textures. =20

   PyMOL's raytracer is really just an optimized orthographic, =
textureless, reflectionless raycaster, which is fine for simple =
molecules, but inadequate for complex scenes.  In other words, to make a =
Science or Nature cover image, you will have to do a bit more work than =
just hitting the "Ray" button. =20

   Specifically, you need to introduce a geometric object behind the =
molecule onto which the shadow can be cast.  If all you need is a flat, =
untextured surface, then you can use PyMOL's CGO module to generate =
this.  Otherwise, you'll need to learn how to modify PyMOL's PovRay =
input file to contain these objects by reading the PovRay documentation =
and editing the text file you already know how to generate.

  I've attached an example below.  Save to "ray.py" and run it from =
within PyMOL. =20

Cheers,
Warren


from pymol.cgo import *

obj =3D [
      BEGIN, TRIANGLE_STRIP,
      COLOR, 0.8,0.7,0.4,
      NORMAL, 0.0, 1.0, 0.0,

      VERTEX, -7.0, -20.0, 0.0,
      VERTEX, -10.0, -20.0, 30.0,

      VERTEX,  12.0, -20.0, 0.0,
      VERTEX,  15.0, -20.0, 30.0,

      END,
      ]

cmd.load_cgo(obj,"plane")
cmd.load("$PYMOL_PATH/test/dat/pept.pdb")
util.ray_shadows('heavy')

cmd.set_view((\
     0.962451875,   -0.074250713,   -0.261098653,\
     0.192369312,    0.865197897,    0.463061303,\
     0.191519246,   -0.495900899,    0.846994936,\
    -0.427299917,    0.681541085,  -83.549995422,\
     1.224037170,  -10.279197693,   20.545440674,\
    70.968811035,  117.627342224,    0.000000000 ))

cmd.ray()

--
mailto:wa...@su...
Warren L. DeLano, Ph.D.

> -----Original Message-----
> From: Robert Campbell [mailto:rl...@k2...]
> Sent: Friday, April 12, 2002 9:52 AM
> To: PyM...@li...
> Subject: [PyMOL] Fancy images
>=20
>=20
> Hi,
>=20
> Someone posed a question to me that I couldn't answer, so I'm=20
> turning to
> the collective wisdom here for help.
>=20
> How does one create one of those fancy journal-cover images in which,
> say, a structure is superimposed on some other image as a background,
> but in which a shadow is cast on the background. There is a=20
> simple image
> of this sort on the opening page of the pymol gallery, so I=20
> figure this
> must be possible and that perhaps Warren himself knows. :)
>=20
> I assume that this might be a povray method, so I figured out=20
> that if do
> something like:
>=20
> 	(header,data) =3D cmd.get_povray()
> 	file=3Dopen('povray.dat','w')
> 	file.write(header)
> 	file.write(data)
> 	file.close()
>=20
> then I have a povray input file that I can render.
>=20
> Does anybody have a recipe for adding a background image using povray?
> Or is there another, better way?
>=20
> Cheers,
> Robert
> --=20
> Robert L. Campbell, Ph.D.              =20
> http://biophysics.med.jhmi.edu/rlc
> rl...@k2...                                    phone:=20
> 410-614-6313
> Research Specialist/X-ray Facility Manager
> HHMI/Dept. of Biophysics & Biophysical Chem., The Johns=20
> Hopkins University
>     PGP Fingerprint: 9B49 3D3F A489 05DC B35C  8E33 F238 A8F5=20
> F635 C0E2
>=20
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>=20