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Nice PovRay settings
I typically use the make_pov.py script and "run" it from pymol once to load the function, and then I do make_pov('povray.inp') to create the povray.inp file. Then I edit that file to insert some lines like:
fog {
distance 10
fog_type 2
fog_alt 10.
fog_offset -160.
up <0.,1.,.4>
colour rgbt<1.0, 1.0, 1.0, 0.1>
turbulence 0.8
}
In this case I'm not really doing depth-cueing but adding fog at the lower background edge (there were two planes defining the background and a surface below the molecule) rising up towards the front upper edge of the scene.
"fog_type 2" means a "rising fog" along the "up" vector. fog_type 1 is a constant fog. To get pure depth cueing, you would want "up" to be along the <0., 0., 1.> vector (I think!). You'll need to play around with the distance and fog_offset parameters. You wouldn't necessarily want the "turbulence" parameter in there either. Check out "Atmospheric Effects" in the povray documentation for many more details: http://www.povray.org/documentation/view/201/
make_pov.py v1
# make_pov.py
# Do "run make_pov.py" from within pymol and then execute the script
# with "make_pov('povray.inp')" to create the povray.inp file.
#
# written by Robert Campbell 2003
#
from pymol import cmd
def make_pov(file):
(header,data) = cmd.get_povray()
povfile=open(file,'w')
povfile.write(header)
povfile.write(data)
povfile.close()
make_pov.py v2
This is a more extended version of an earlier extension of the version by Robert Campbell. The scene is written in two parts, a .pov file containing all meta data, such as the lights, camera and #defaults, and an include file (.inc) which contains the structure. In this way you have maximum control over your scene without having to edit a huge povray file. You may even want to consider splitting your scene up in separate parts (taken from the same perspective), which you combine in a global .pov file using #include statements. This will give even more control with regards to modifications to the scene. If 'clip' is set to near|far|both, then the corresponding clipping plane(s) is/are included in a CSG difference object. Note that the result may increase the render time significantly unless the scene is simple.
Once you run run make_pov.py, run make_pov to execute the script.
NB. the .pov file contains a commented statement with regards to a povray macro file, which allows transforming scenes and objects from model space to camera space and vice versa. The macro file is given below.
# make_pov.py
# Do "run make_pov.py" from within pymol and then execute the script
# with "make_pov('povray.inp')" to create the povray.inp file.
#
# Original script written by Robert Campbell
# Modified by Tsjerk A. Wassenaar
#
from pymol import cmd
def make_pov(file, name="PymolObject", meta=True, clip=False ):
f1, f2 = file, file[:-4] + '.inc'
(header,data) = cmd.get_povray()
povfile = open(f1,'w')
if meta: povfile.write(header)
povview = cmd.get_view()
if clip:
objtype = "difference"
objclip = ""
if clip in ["near","both"]:
objclip = objclip + "plane { z, -%f }" % povview[15]
if clip in ["far","both"]:
objclip = objclip + "plane { z, -%f }" % povview[16]
else:
objtype = "object"
objclip = ""
povfile.write("""\n
// Uncomment the following lines if you have the pymolmacro.inc include file and want to use it.
/*
#include \"pymolmacro.inc\"
PYMOL_VIEW( %10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f,
%10.5f, %10.5f, %10.5f )
*/
""" % povview)
povfile.write("""
#declare %s = union { #include "%s" }
%s { %s %s }
""" % (name, f2, objtype, name, objclip ) )
povfile.close()
povfile = open(f2,'w')
povfile.write(data)
povfile.close()
cmd.extend('make_pov',make_pov)
//
// PYMOLMACRO.INC v0.2
//
// (c)2005 Tsjerk Wassenaar, University of Groningen
//
// This include file for Povray contains
// just a few macros which together allow
// the conversion between the model space
// (cartesian coordinates) and the Pymol
// camera space.
//
// With these macros one can easily combine
// a Pymol scene with objects defined in the
// coordinate space of the original
// structure file.
//
// The input consists of the output of the
// get_view() command in Pymol. This output
// consists of 18 floating point numbers
// defining a rotation matrix and shift
// vectors for the origin of rotation and
// for the camera position.
//
// The macro PYMOL_VIEW loads a
// view obtained from Pymol.
//
// It #declares two transformation statements:
//
// FROM_PYMOL_VIEW
// TO_PYMOL_VIEW
//
// The first can be used to transform the Pymol
// scene back to model (normal) space, the latter
// is used to transform other objects to appear in
// the scene on the correct position.
//
// Additionally four macros are defined to transform
// vectors (points) from one space to another:
//
// VEC2PYMOLSPACE( <x, y, z> )
// VEC2CARTSPACE( <x, y, z> )
// VEC2PYMOLVEC( <x, y, z> )
// VEC2CARTVEC( <x, y, z> )
//
// *NEW*
//
// If the view from pymol is stored as an array:
//
// #declare M = array[18] {...}
//
// then the macros
//
// SET_PYMOL_VIEW
// and
// UNSET_PYMOL_VIEW
//
// can be used directly to transform objects to and from that view:
// object { ... SET_PYMOL_VIEW( M ) }
//
// This is especially useful if multiple views are defined
// and the scene was set in one:
//
// #declare VIEW1 = M;
// #declare VIEW2 = N;
// union { #include "file.inc" UNSET_PYMOL_VIEW( M ) SET_PYMOL_VIEW( N ) }
//
// NOTE: transform statements are combined by POV-Ray prior to
// transformations of objects, so there's little need to implement a macro
// SWITCH_PYMOL_VIEW( M, N )
// although that would appear simpler in the scenes
// Tsjerk A. Wassenaar
// February 16, 2005
// April 5, 2005
// September 2, 2009
//
// Determinant of a matrix
//------------------------
#macro DET( M )
#local a = M[0] * ( M[4]*M[8] - M[5]*M[7] );
#local b = M[1] * ( M[3]*M[8] - M[5]*M[6] );
#local c = M[2] * ( M[3]*M[7] - M[4]*M[6] );
(a - b + c)
#end // of DET()
// The inverse of a matrix
//------------------------
#macro INV( m11, m12, m13, m21, m22, m23, m31, m32, m33 )
#local M = array[9] { m11, m12, m13, m21, m22, m23, m31, m32, m33 };
#local invdet = 1/DET( M );
#local t11 = invdet * ( m22*m33 - m23*m32 );
#local t12 = invdet * ( m13*m32 - m12*m33 );
#local t13 = invdet * ( m12*m23 - m13*m22 );
#local t21 = invdet * ( m23*m31 - m21*m33 );
#local t22 = invdet * ( m11*m33 - m13*m31 );
#local t23 = invdet * ( m13*m21 - m11*m23 );
#local t31 = invdet * ( m21*m32 - m22*m31 );
#local t32 = invdet * ( m12*m31 - m11*m32 );
#local t33 = invdet * ( m11*m22 - m12*m21 );
t11, t12, t13, t21, t22, t23, t31, t32, t33, 0, 0, 0
#end // of INV()
#macro M_INV( M )
#local invdet = 1/DET( M );
#local t11 = invdet * ( M[4]*M[8] - M[5]*M[7] );
#local t21 = invdet * ( M[2]*M[7] - M[1]*M[8] );
#local t31 = invdet * ( M[1]*M[5] - M[2]*M[4] );
#local t12 = invdet * ( M[5]*M[6] - M[3]*M[8] );
#local t22 = invdet * ( M[0]*M[8] - M[2]*M[6] );
#local t32 = invdet * ( M[2]*M[3] - M[0]*M[5] );
#local t13 = invdet * ( M[3]*M[7] - M[4]*M[6] );
#local t23 = invdet * ( M[1]*M[6] - M[0]*M[7] );
#local t33 = invdet * ( M[0]*M[4] - M[1]*M[3] );
array[9] {t11, t12, t13, t21, t22, t23, t31, t32, t33}
#end
#macro MV_MUL( M, V )
< M[0]*V.x + M[1]*V.y + M[2]*V.z,
M[3]*V.x + M[4]*V.y + M[5]*V.z,
M[6]*V.x + M[7]*V.y + M[8]*V.z >
#end
#macro SET_PYMOL_VIEW( M )
transform {
translate -< M[12], M[13], M[14] >
matrix < M[0], M[1], M[2],
M[3], M[4], M[5],
M[6], M[7], M[8],
M[9], M[10], M[11] >
}
#end // of SET_PYMOL_VIEW
#macro UNSET_PYMOL_VIEW( M )
transform {
translate -< M[9], M[10], M[11] >
matrix < INV( M[0], M[1], M[2], M[3], M[4], M[5], M[6], M[7], M[8] ) >
translate < M[12], M[13], M[14] >
}
#end // of UNSET_PYMOL_VIEW
#macro C2P_VEC( M, vec)
#local nvec = vec - <M[12],M[13],M[14]>;
#local nvec =
< M[0]*nvec.x + M[1]*nvec.y + M[2]*nvec.z,
M[3]*nvec.x + M[4]*nvec.y + M[5]*nvec.z,
M[6]*nvec.x + M[7]*nvec.y + M[8]*nvec.z >;
nvec + <M[9],M[10],M[11]>
#end
#macro P2C_VEC( M, vec)
MV_MUL( M_INV(M), vec - <M[9],M[10],M[11]> ) + <M[12],M[13],M[14]>
//#local nvec = vec - <M[9],M[10],M[11]>;
//#local N = M_INV( M ) ;
//#local nvec =
// < N[0]*nvec.x + N[1]*nvec.y + N[2]*nvec.z,
// N[3]*nvec.x + N[4]*nvec.y + N[5]*nvec.z,
// N[6]*nvec.x + N[7]*nvec.y + N[8]*nvec.z >;
//nvec
#end
#macro PYMOL_VIEW( r11, r12, r13, // 3x3 Rotation matrix ( Model space to Camera space )
r21, r22, r23,
r31, r32, r33,
c1, c2, c3, // Camera position ( Model space )
o1, o2, o3, // Origin of rotation ( Model space )
s1, s2, or) // Slab near and far, orthoscopic flag ( discarded )
#declare PYMOLVIEW_RMATRIX = array[9] { r11, r12, r13,
r21, r22, r23,
r31, r32, r33 }
#declare PYMOLVIEW_CAMPOS = < c1, c2, c3 >;
#declare PYMOLVIEW_ORGPOS = < o1, o2, o3 >;
#declare TO_PYMOL_VIEW = transform {
translate -< o1, o2, o3 >
matrix < r11, r12, r13,
r21, r22, r23,
r31, r32, r33,
c1, c2, c3 >
}
#declare FROM_PYMOL_VIEW = transform {
translate -< c1, c2, c3>
matrix < INV( r11, r12, r13, r21, r22, r23, r31, r32, r33 ) >
translate < o1, o2, o3>
}
#macro VEC2PYMOLSPACE(vec)
#local nvec = vec - PYMOLVIEW_ORGPOS;
#local nvec =
< PYMOLVIEW_RMATRIX[0]*nvec.x + PYMOLVIEW_RMATRIX[3]*nvec.y + PYMOLVIEW_RMATRIX[6]*nvec.z,
PYMOLVIEW_RMATRIX[1]*nvec.x + PYMOLVIEW_RMATRIX[4]*nvec.y + PYMOLVIEW_RMATRIX[7]*nvec.z,
PYMOLVIEW_RMATRIX[2]*nvec.x + PYMOLVIEW_RMATRIX[5]*nvec.y + PYMOLVIEW_RMATRIX[8]*nvec.z >;
nvec + PYMOLVIEW_CAMPOS
#end
#macro VEC2CARTSPACE(vec)
#local nvec = vec - PYMOLVIEW_CAMPOS;
#local R = PYMOLVIEW_RMATRIX;
#local invdet = 1/DET( R );
#local T = array[9];
#local T[0] = invdet * ( R[4]*R[8] - R[5]*R[7] );
#local T[1] = invdet * ( R[2]*R[7] - R[1]*R[8] );
#local T[2] = invdet * ( R[1]*R[5] - R[2]*R[4] );
#local T[3] = invdet * ( R[5]*R[6] - R[3]*R[8] );
#local T[4] = invdet * ( R[0]*R[8] - R[2]*R[6] );
#local T[5] = invdet * ( R[2]*R[3] - R[0]*R[5] );
#local T[6] = invdet * ( R[3]*R[7] - R[4]*R[6] );
#local T[7] = invdet * ( R[1]*R[6] - R[0]*R[7] );
#local T[8] = invdet * ( R[0]*R[4] - R[1]*R[3] );
< T[0]*nvec.x + T[3]*nvec.y + T[6]*nvec.z + PYMOLVIEW_ORGPOS.x,
T[1]*nvec.x + T[4]*nvec.y + T[7]*nvec.z + PYMOLVIEW_ORGPOS.y,
T[2]*nvec.x + T[5]*nvec.y + T[8]*nvec.z + PYMOLVIEW_ORGPOS.z >
#end
#macro VEC2PYMOLVEC(vec)
< PYMOLVIEW_RMATRIX[0]*vec.x + PYMOLVIEW_RMATRIX[3]*vec.y + PYMOLVIEW_RMATRIX[6]*vec.z,
PYMOLVIEW_RMATRIX[1]*vec.x + PYMOLVIEW_RMATRIX[4]*vec.y + PYMOLVIEW_RMATRIX[7]*vec.z,
PYMOLVIEW_RMATRIX[2]*vec.x + PYMOLVIEW_RMATRIX[5]*vec.y + PYMOLVIEW_RMATRIX[8]*vec.z >
#end
#macro VEC2CARTVEC(vec)
#local nvec = vec - PYMOLVIEW_CAMPOS;
#end
#macro CAM2PYMOLCAM()
#end
#macro CAM2CARTCAM()
#end
#end