VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jul 08 2013 - 15:16:20 CDT
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- In reply to: Tristan Croll: "RE: secondary structure works on linux, it doesn't work on Mac in certain structures"
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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/
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- Previous message: Mayne, Christopher G: "Re: reg interaction energy"
- In reply to: Tristan Croll: "RE: secondary structure works on linux, it doesn't work on Mac in certain structures"
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