VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 15 2021 - 11:51:36 CDT

Carlos,
  Since you are already aware of the option to use ssrecalc when needed,
I'm not sure what might be going on here.

VMD just uses the results provided to it from STRIDE, so the big question
here is why STRIDE is giving a different result than before.

I do know that STRIDE has some sensitivity to coordinates that are far
away from the origin, so if you've loaded the same structure, but it had
been aligned or something else that brought it closer to the origin
previously, that might play a factor in what you're describing.

If you're not happy with what STRIDE is doing, the new versions of VMD
can also call xDSSP/HSSP etc rather than STRIDE if you happen to have those
installed.

Worst-case, if you have good secondary structure assignments
from another source, you can set the secondary structure assignments
manually, overriding what STRIDE or other tools have calculated,
if necessary.

Best,
  John

On Tue, Apr 13, 2021 at 05:28:22PM -0400, Carlos Simmerling wrote:
> hi all,
> odd problem, I was using VMD on a large system and it worked fine, my
> secondary structures made sense and I could use ssrecalc when needed.
> However, I was doing a render with tachyon that crashed, and now I cannot
> seem to get vmd/stride to show the same helices that it did before. many
> segments are shown as coil and ssrecalc changes things a bit, but never
> adds the full helices that I was getting before. This could just be
> coincidence that it happened after a crash, but does anyone have ideas?
> Same coordinate sets, it just doesn't work any more.
> vmd 1.94a51 64 bit on windows 10.Â
> carlos 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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