VMD-L Mailing List

From: Tristan Croll (tristan.croll_at_qut.edu.au)
Date: Wed Jul 03 2013 - 23:50:03 CDT

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