VMD-L Mailing List

From: Guo Zhi (gzgzgz_at_gmail.com)
Date: Wed Mar 21 2007 - 03:32:37 CDT

Thanks john, I will try that.

2007/3/21, John Stone <johns_at_ks.uiuc.edu>:
> 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
> 

-- 
Guo Zhi