VMD-L Mailing List

From: Shirley Li (li19104_at_yahoo.com)
Date: Mon Aug 09 2004 - 20:51:00 CDT

Hi Mr. Stone,
 
Thank you so much for your kind help with my questions.
 
For question 3), yes, I DO need to play the movie back SLOWER than 1 frame per second, so that I could see what exactly happens, for example, I want it to be five times SLOWER than 1frame per second. I wonder if it is possible.
 
Thank you again for your help.
 
Regards,
 
Shirley

John Stone <johns_at_ks.uiuc.edu> wrote:

Hi,

On Sun, Aug 08, 2004 at 05:26:56PM -0700, Shirley Li wrote:
> 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?

If you're structure contains only atoms, then you would use "Surf" or "MSMS"
in order to see the solvent-accessible or solvent-exluded surface.
The "Isosurface" representation is only used for volumetric data such
as in potential/density map display.

> 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?

You can write a Tcl script that loads structures, or adds trajectories.
A relatively simple script that you can learn from is located here:
http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/animatepdbs/

> 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?

I'm not sure I understand your problem.
The speed control will slow down the trajectory playback to 1 frame
per second or thereabouts. Do you need to play it back slower than that???
What speed are you referring to in the OpenGL window, the "FPS"??
The FPS only tells you how fast the video card can draw the scene, and
has nothing to do with the rate at which a trajectory is animated.
How slow do you need VMD to play your trajectory?

John Stone
vmd_at_ks.uiuc.edu 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 
WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
		
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