Another tips is to open the vrml file with 3D modelling
program (for example, Blender) and remove redundant
vertices. It is called "Remove Doubles" in Blender.

PyMOL tends to define discrete vertices even when their 
coordinates are identical.

See http://www.pymolwiki.org/index.php/Blender for details.

Best regards,

Takanori Nakane

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