From: Jordi Faraudo (
Date: Fri Nov 11 2011 - 06:04:50 CST


we are trying to visualize with VMD a simulation in which the fields occupancy or beta are employed to store data which we would like to see as color scale.
The important point is that the values of these fields *** change*** at every frame.

If we upload a single simulation frame with VMD, the obtained visualization is correct (= the color scale reflects the actual value of occupancy for each atom). However, if we upload a full pdb trajectory , VMD only uses the value of the first frame and the colors are not updated at each frame, in spite of selecting the options "update color every frame " and "update selection every frame".

Apparently, VMD is not aware of changes of occupancy (or beta) during the trajectory. For example, if we load the full trajectory (which has different values of occupancy at each frame) and then we save it with VMD we get a trajectory in which the occupancy/beta fields have the same values in all frames.

Anyone has any idea of how to solve this?


Dr. Jordi Faraudo 
Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC) 
Campus de la UAB 
E-08193 Bellaterra (Spain) 
*** NEW TEL. NUMBER: 931 88 87 86