VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jul 08 2013 - 15:16:20 CDT

Hi,
  If you have trouble with STRIDE, you can tell VMD to force STRIDE
to recompute secondary structure later using the "mol ssrecalc" command...
If it has failed, VMD won't automatically retry later, but if you edit
the structure as proposed below, you can manually trigger the recalc
using the text commands.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jul 04, 2013 at 02:50:03PM +1000, Tristan Croll wrote:
> 1iw7 is a very big structure - I'd guess that most likely you're out of
> memory. Stride always seems to be the first to fail as RAM becomes
> limited. I note that for some reason 1iw7 contains two copies of the
> structure at a very substantial distance from each other - why not try
> deleting one and reloading? Note that once Stride has collapsed it won't
> come back unless you quit and restart VMD.
>
>
>
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf
> Of Juan Felipe Ortiz
> Sent: Wednesday, 3 July 2013 2:24 AM
> To: vmd-l_at_ks.uiuc.edu
> Subject: vmd-l: secondary structure works on linux, it doesn't work on Mac
> in certain structures
>
>
>
> I am trying to work on structure 1iw7 from the pdb in VMD
> The secondary prediction (stride) works just fine in a Linux machine.
> However, secondary prediction (colors, cartoons, annotation in sequence
> viewer, etc) doesn't work in a Mac.
> I thought that the problem was the installation, but in that same Mac,
> secondary prediction is just fine for structure 1ubq
> What can be happening?
>
> thank you
>
> Juan Felipe Ortiz 

-- 
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/