Visualizing PDB file in VMD, how to upload molecules? Problem: When I load PDB-file of my protein of interest in VMD, nothing happens. The molecules is uploaded, but when I push "D" the screens with with big "VMD" letter freezes instead of presenting the structure of the protein in the PDB file. This is what is looks like:



Any Ideas what causes this? Should the PDB file be in a specific folder? I am a complete novice at this, so I wont understand very complicated answers.

I have downloaded the mac version of VMD version 1.9.2, I have Mac OS X version 10.11.2.  Here is the PDB file that I want to open.
I found a shortcut, and that is if I go to (click on):


file
New Molecule
Enter in the "browser" window the direct PDB accession code "3WD5" (for my protein) then VMD retrieved the protein structure form the PDB database on its own, and is showing it as it should in the visualization window. 


However, this does still not resolve why it will not load a downloaded PDB file, but I suspect its most likely due to some problem with downloading of the files or installing the program its self that has gone wrong.