This file is indexed.

/usr/share/pymol/data/shaders/default.vs is in pymol 1.7.2.1-1.

This file is owned by root:root, with mode 0o644.

The actual contents of the file can be viewed below.

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varying vec3 N, L0, H0, L1, H1;
varying vec4 D0, A0, D1, A1;
varying float fog;

varying vec3 fog_color;

uniform bool lighting_enabled;

uniform bool bg_gradient;
uniform vec3 fog_color_top;
uniform vec3 fog_color_bottom;

void main()
{
  N = normalize(gl_NormalMatrix * gl_Normal);
  vec3 eye_pos = vec3(gl_ModelViewMatrix * gl_Vertex);
  vec3 aux = vec3(gl_LightSource[0].position - vec4(eye_pos, 1.0));
  if (lighting_enabled){
    L0 = normalize(aux);
    H0 = normalize(gl_LightSource[0].halfVector.xyz);
    aux = vec3(gl_LightSource[1].position - vec4(eye_pos, 1.0));
    L1 = normalize(aux);
    H1 = normalize(gl_LightSource[1].halfVector.xyz);
    A0 = gl_LightSource[0].ambient * gl_Color;
    D0 = gl_LightSource[0].diffuse * gl_Color;
    A1 = gl_LightSource[1].ambient * gl_Color;
    D1 = gl_LightSource[1].diffuse * gl_Color;
    A0.a = gl_Color.a;
    A1.a = 0.;
  } else {
    A0 = gl_Color;
  }
  gl_FogFragCoord = -eye_pos.z;
  fog = (gl_Fog.end - gl_FogFragCoord) * gl_Fog.scale;
  gl_Position = gl_ModelViewProjectionMatrix * a_Vertex;
  if (bg_gradient){
    fog_color = mix(fog_color_bottom, fog_color_top, (1. + gl_Position.y/gl_Position.w)/2.);
  } else {
    fog_color = fog_color_top;
  }
  gl_Position = ftransform();
}