[PyMOL] Pymol & 3D printing

[Chris W. <cw...@ua...>]

Hello,

My name is Chris Want, and I do visualization support at
the University of Alberta -- and in particular I run the
university's 3D printer.

I'm not a pymol user per se, but I have had a
client who really liked the 'surface' visualization
from pymol and wanted to print some molecules off
on the 3D printer. Unfortunately, pymol lacks an
export export option for the 'STL' format, so
I crafted together a little hack that quietly dumps
out an STL file when a surface is created, which I
hope may be of use to other users (or perhaps somebody
who finds it useful, and who also has an
understanding of the pymol user interface
code, can create a button for it).

Here it is (sorry it's not in a proper 'diff'
format -- I'm not using cvs code):

File layer2/RepSurface.c, 2 modifications:

1) Add this function:

void DumpStlAscii(char *filename, RepSurface *I) {
   FILE *fpSTL;
   float *x, *y, *z;
   int a;

   fpSTL = fopen(filename, "wb");
   fprintf(fpSTL, "pymol molecule\n" );

   for (a=0; a < I->NT; ++a) {
     x = I->V + 3*((I->T)[3*a]);
     y = I->V + 3*((I->T)[3*a+1]);
     z = I->V + 3*((I->T)[3*a+2]);

     /* We'll let whatever app opens this file
      * deal with the face normals.
      */
     fprintf(fpSTL,
             "  facet normal 0.0 0.0 0.0\n"
             "    outer loop\n"
             "      vertex %g %g %g\n"
             "      vertex %g %g %g\n"
             "      vertex %g %g %g\n"
             "    endloop\n"
             "  endfacet\n",
             x[0],x[1],x[2],
             y[0],y[1],y[2],
             z[0],z[1],z[2]);
   }
   fprintf(fpSTL, "endsolid\n" );
   fclose(fpSTL);

}

2) In the function RepSurfaceNew(),
locate these lines:

       PRINTFB(FB_RepSurface,FB_Details)
         " RepSurface: %i triangles.\n",I->NT
         ENDFB;

Add the following function call immediately
after the above lines:

       DumpStlAscii("/tmp/pymol.stl", I);



Now, when the 'surface' is calculated, it's geometry
is dumped to the file /tmp/pymol.stl.


I Hope this is useful to somebody!

Regards,
Chris

P.S. I wish this mailing list had archives ...

-- 
Chris Want
Research Computing Support
Computing & Network Services
University of Alberta
Tel: 1-780-492-9418