VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 20 2016 - 16:17:47 CDT

Hi Brian,
  Interesting. Can you send me a copy of the broken file to use
for testing? I think you've stumbled across a particular failure
mode that has never arisen before. It would probably be easy for
me to add some sanity checks that would get used for all small
structures. A simple for loop with isnan() checks would catch this
before going into bond determination code. That being said, if the
reason is due to a misformatted file, it should get caught earlier,
in the PDB reader itself. If you can share the broken file, or
a file that emulates whatever is wrong with the broken one, I am
happy to look into that.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Sep 20, 2016 at 06:47:26PM +0000, Bennion, Brian wrote:
> Hello
> Just curious if there is a reason not to include some minor error checking
> in the vmd pdb reader for the coordinate columns.
>
> I ran into a situation where a pdb file is generated in an upstream
> application, and for reasons that are being looked into, the xyz columns
> are all NaN in a very few files (1 out of 300K or so).
>
> This "bug" found this while using vmd in batch mode to do some analysis
> and vmd was hanging at the distance check after a couple hours of running
> the analysis.
>
> The vmd version is 1.9.2 so maybe this is not an issue in newer releases?
>
> Thanks
> Brian Bennion 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
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