From: Shirley Li (
Date: Sun Aug 08 2004 - 19:26:56 CDT

I'm a new user to VMD, while I like it because it has many functions and has friendly interface. I have some questions here:
1) In order to identify the locations of the polar/non-polar/charged residues in a protein, I would like to display the molecule surface of the protein. For this purpose, should I choose the "surface" or "isosurface" drawing type? In the "color method" panel, should I use "Typ" or "ResType"? How are colors assigned for polar/non-polar/charged residues?
2) In order to analyze multiple trajectory files, how to import these trj files all at once instead of one by one? Could anybody kindly provide me with a script? My .trj files have names as dyn1.trj, dyn2.trj, dyn3.trj, ..., dyn50.trj, and the name of my PSF file is dyn.psf. Once I have such script, how to apply it?
3) The third question is about the speed of animations made with VMD. It seems that VMD does NOT provide the control of the update speed between two frames in the ANIMATION, although VMD provides option to change the speed for PLAYBACK before making the animation. Even though I draw the speed bar to the leftmost and I set the update step as 1 in the "VMD main" window, the speed of my animation is too fast. It seems that the speed in the animation is DIFFERENT from the speed shown in the "VMD main" window and in the "openGL display" window. Could anybody help me to slow it down?
Any help and suggestions will be appreciated.

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