VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 25 2015 - 09:25:11 CST
Unfortunately STRIDE uses some quadratic time algorithms, so for large
structures it becomes completely unusable, aside from its other problems.
We have a prototype replacement for STRIDE that resolves these problems
and others, but it's not quite ready for prime time yet.
On Wed, Nov 25, 2015 at 08:04:50AM +0000, Tristan Croll wrote:
> Hi all,
> I've done some tinkering with the STRIDE source code and with VMD's
> Stride.C interface, and I seem to have them playing nicely together for
> large structures. The only downside is that Stride starts getting veeerrry
> slow as the structure size increases (almost a full minute for my ~17,000
> residue test case). Give me a yell if you want a copy.
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/