VMD-L Mailing List

From: Martin K. Jones (mkjones_at_aging.uab.edu)
Date: Fri Oct 02 2009 - 17:00:12 CDT

Hi John,

Thanks for your message and explanation. I did upgrade to 1.8.7 and
still have the problem. I was going to provide image and example but
with your comments I do not think they are necessary. If field widths
are the problem, I believe STRIDE is failing if any coordinate is <=
-100.0. Similarly, I would guess that coordinates >= 1000.0 would also
cause failure. I will need to write a script to translate my trajectory
so that all coordinates are within these bounds.

Thanks,
Martin
_____________
 
Martin K Jones
University of Alabama at Birmingham
 

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Friday, October 02, 2009 4:25 PM
To: Martin K. Jones
Cc: vmd-l_at_ks.uiuc.edu
Subject: Re: vmd-l: RE: Problems with Stride

Martin,
  I don't think that you'll see any difference in behavior, but
yes, I think that upgrading to the latest version is a wise move
for many other reasons. See the note I just sent as to my theory
on the reasons for this problem with STRIDE. We didn't develop STRIDE,
it was written by a different group, so as Axel already mentioned,
at some point someone or some group needs to either do some maintenance
on it, or perhaps write a new program to replace it.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Oct 02, 2009 at 01:16:54PM -0500, Martin K. Jones wrote:
> Sorry, I thought I saw a message from John Stone that seemed to
indicate that it was a known problem. I've tried to find that message
again, but haven't so far. I will upgrade to 1.8.7 and see if the
problem is remedied. If not I will return with more information. Thanks
for your suggestions.
>
> Martin
>
> _____________
>
> Martin K Jones
> University of Alabama at Birmingham
>
>
> -----Original Message-----
> From: Axel Kohlmeyer [mailto:akohlmey_at_gmail.com]
> Sent: Friday, October 02, 2009 1:07 PM
> To: Martin K. Jones
> Cc: vmd-l_at_ks.uiuc.edu
> Subject: Re: vmd-l: Problems with Stride
>
> On Fri, 2009-10-02 at 12:18 -0500, Martin K. Jones wrote:
>
> martin,
>
> > I???m using VMD 1.8.6 on Windows XP, and it seems that stride can
fail
> > to calculate correctly if the coordinates of my molecule are outside
> > of some as yet to be determined bounds. The problem is, I have not
> > seen any error messages displayed with regard to this failure. In my
> > case, roughly half of my molecule gave incorrect results with
stride.
>
> how should anybody be able to help you with this?
>
> please keep in mind that a) stride is shipped with VMD, but
> not really maintained by the VMD developers (it is effectively
> unmaintained and if somebody would step up and implement the
> stride algorithm or something better(?) to be run from within
> VMD, it would be _highly_ welcome), and that b) you don't
> provide and means to reproduce your problems, e.g. file(s)
> and screenshots and an explanation what you expect and what
> you get instead.
>
> cheers,
> axel.
>
> p.s.: the current version of VMD is 1.8.7. due to the long
> time since the release of 1.8.6, it is possible that
> you have run into a known and fixed problem.
>
> >
> >
> > Thanks,
> >
> > Martin
> >
> >
> >
> > _____________
> >
> >
> >
> > Martin K Jones
> >
> > University of Alabama at Birmingham
> >
> >
> >
> >
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
> 

-- 
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