Rendering 3D Surveys with Pymol

Jarvist Moore Frost jarvist at
Wed Oct 5 18:04:13 BST 2011

Dear Survex users,

I thought you may be interested in a cludge I developed a few weeks
ago to go from Survex .3d file to Pymol (a free, python based, 3D
molecule viewer heavily used in the computational biology community).
Pymol is a very nice tool to make pretty renders, an also has a number
of 3D display modes (including anaglyphs, shutter glasses and
cross-eye / wall-eye stereo).

Code, and a link to a high-def youtube vid of the resulting ray trace
movie is available here:

As usual, the program started around midnight being as general as
possible, then had ever more specific hacks hardcoded in. Never the
less, it does colouring by depth on the HSV colour wheel, includes a
set of cardinal axes, and estimates survey shot passage dimension
based on the shot length.

At some point, I'd quite like to add a chequerboard grid, and expose
more details of the survey to pymol as attributes so that you can use
the nice python tools to do fun things such as take over the colouring
(for instance, a rainbow colour scheme based on survey trip?), expose
the station labels, perform RMSD fits & distance calculations etc.

I also have some python code that generates .svx files for DEM data
from a text-based ASCII Tuple format (originally converted from some
proprietary geo stats format). I've found that a mixture of grid based
DEM data, as well as contour-like (or rather, traces) parallel lines
over the mountain range. Drop me an email if you think this may be
useful, and I'll package it up.

May your surveys rotate in a manner truly sublime,


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