VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Wed Nov 25 2015 - 16:49:34 CST

Hi John,

A short-term easy work-around would be to write a copy of the output file to the working directory, so STRIDE only needs to be called the first time the structure is loaded and when a recalculation is explicitly called for. Whether it's worthwhile to do so depends on how far your replacement is progressed.

Cheers,

Tristan

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Thursday, 26 November 2015 1:25 AM
To: Tristan Croll
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: Stride for large structures

Tristan,
  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.

Cheers,
  John

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.
>
>
>
> Cheers,
>
>
>
> Tristan 

--
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/