VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 21 2007 - 01:42:15 CDT

Hi,
  I'm forwarding your note to the author of the Contact Map plugin
in case he has suggestions on this. I believe I'm the one that
added the text comment to the source file about the buggy behavior,
and that this is why that functionality is not exposed to the graphical
interface, as I recall. Unless Barry (the author) has time to look
into this in the short-term, you might be better off using his script
as a "guide" and write your own implementation. I think a version that
just outputs the matrix to text would be far easier to write/debug than
the graphical version that Barry wrote, so this would be one reason to
develop your own script. It would likely be faster as well, and since
this is an O(N^2) type of computation (or O(NlogN) if you use an acceleration
data structure), I suspect you'd be much better off doing your own version
if you have big structures to process.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 20, 2007 at 10:18:03PM +0800, Guo Zhi wrote:
> Hi,
> I wish to output the residue distance matrix data, to save it
> in the format of numerical data in a text file rather than the default
> snapshot function in contactmap plugin. I found a function called
> writeDataFile() in the source, but as its comment says, it can not
> work normally, always missing some data when I tried to use it. Does
> anyone have got a better solution? Thanks.
>
> Guo Zhi 

-- 
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