VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 22 2003 - 23:18:11 CDT

Hi Dongsheng,
  I have a few answers for you on the items you brought up:

1) It sounds like you're getting warnings from VMD because it is
   having to use its distance-based bond search algorithm to determine
   connectivity rather than a PSF file. (The current PDB plugin doesn't
   yet parse the PDB "CONECT" records, though this is high on the list of
   things to improve in the PDB plugin) You can create a PSF file from
   your PDB file with this IRIX program, which should eliminate
   those warnings (load the PSF first, then the PDB file(s)):
     http://www.ks.uiuc.edu/Development/MDTools/conect2psf/

2) The 'vmdmovie' plugin is currently constrained to operate at
   the basic MPEG frame rates which are 24fps, 25fps, and 30fps.
   You can slow down the rate of animation by duplicating frames in
   your trajectory. In a future version of the 'vmdmovie' plugin, I
   intend to have an option to do this automatically. This only gives
   you a way to cut the displayed rate by some integer factor, to do
   other rates requires some other techniques to get decent results.

   If you truly require a framerate other than 24/25/30, then building
   the movie on Windows with VideoMach as an AVI, or by running an external
   movie tool on the individual images produced by 'vmdmovie' would be
   your best option. (Adobe Premiere will load the frame sets produced
   by 'vmdmovie' for example)

Let us know if you need more help with these items.
Sorry for the delayed reply, I've been swamped preparing VMD 1.8.1 for
release.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, May 21, 2003 at 11:13:52PM -0500, Dongsheng Zhang wrote:
> To Whom It May Concern,
>
> I am a new user of VMD. I have two questions. One is for displaying.
> Another one is for making a movie.
>
> 1. I got some trajectory files in YASP format (it is a binary file, I
> can't show you the format) for model polymer crystallization. Because
> there is no real atom in polymer, it seems hard to display it. I have
> done it successfully for short chains by the following process: first
> transfer YASP file to PDB file by using poly2pdb. The format is
>
>
> REMARK 4 Generated by poly2pdb
> REMARK 4 Description:
> HETATM 1 C UNX 1 15.707 -11.100 9.006
> TER 2 UNX 1
> HETATM 3 C UNX 1 15.691 -10.659 9.254
> TER 4 UNX 1
> HETATM 5 C UNX 1 15.662 -10.191 9.417
> TER 6 UNX 1
> HETATM 7 C UNX 1 15.585 -9.739 9.612
> TER 8 UNX 1
> .
> .
> .
> CONECT 1 3
> CONECT 3 1 5
> CONECT 5 3 7
> CONECT 7 5 9
> .
> .
> .
> MASTER 2 0 0 0 0 0 0 0 19200 19200 19200 0
> END
>
> If I display this directly, the error message is
> MolAtom 14457: Exceeded maximum number of bonds (8).
>
> Therefore I transfer this PDB file to XYZ file, modify the distance
> between two monomers, change the atom type to Oxygen, and transfer XYZ
> file to PBD file by babel. For a system with short chains (20 monomers),
> it works fine. I can make a movie by making a dcd file. However, for
> long chains (100 monomers), it doesn't work, but it surprised me that it
> seems be able to display 10 chains, but not the whole system (192
> chains). Could you please tell me how to use VMD for model polymer?
>
> 2. How to adjust the speed for movie? If I use vmdmovie from tools manu
> and save it as mpg file. It shows too fast. Could you please tell me how
> to adjust it? Can I modify the movie script? If I can, please give me
> some hints.
>
>
> Thank you very much for your help!
>
>
>
> Dongsheng Zhang 

-- 
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