VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 05 2009 - 21:08:57 CDT

Martin,
  I think that if you translate your structure towards the origin
that will ameliorate your problems with STRIDE. I don't think I'll
have time to do anything in the near future, but if a miracle happens
and I find myself with some free time this year, I may see about
hacking the STRIDE code to read from another (non-PDB) file format.
If someone else feels like looking for solutions to this problem,
I would of course welcome that too. So far I haven't heard of any
usable alternative to STRIDE that's also free, but if anyone hears
of something, let me know.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Oct 02, 2009 at 05:00:12PM -0500, Martin K. Jones wrote:
> 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 

-- 
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