VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Nov 11 2011 - 07:34:53 CST

Jordi,

On Nov 11, 2011, at 7:44 AM, Jordi Faraudo <jfaraudo_at_icmab.es> wrote:

Hi,

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?

This is a well known behavior of VMD due to an optimization assuming that
this type of property is usually not present in trajectory files. It has
been discussed many times on this mailing list. Please search the mailing
list archives for previous discussions on the subject of visualizing time
varying per atom preperties in VMD.

Cheers,
      Axel

Jordi 

-- 
Dr. Jordi Faraudo
Institut de Ciencia de Materials de Barcelona (ICMAB-CSIC)
Campus de la UAB
E-08193 Bellaterra (Spain)
http://www.icmab.es/icmab/personnel/detail/593.html
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