.pdb causes avogadro to crash

General Discussion Support
1

I am trying to load .pdb files into avogadro but each time i do the programme crashes.
here is a debug message from visual studios
Unhandled exception at 0x77320DA2 (KernelBase.dll) in avogadro.exe: 0xC00000FD: Stack overflow (parameters: 0x00000001, 0x0EEA2FFC). occurred

Does anyone know a solution to this?

2

further to this i have found this error
No symbol file loaded for openbabel-2.dll

3

It would really help to know:

  • What version of Avogadro you’ve downloaded?
  • What version of Windows you’re using

It would also help to have an example of the PDB file. Are you opening a file from disk or from the Import -> Fetch from PDB command?

4

I am using Avogadro version 1.2.0 with windows 10 professional version 1709
I am opening the pdb file from the disk, it opens fine in UCSF Chimera but not avogadro.

5

Is there an easy way for me to send you the pdb file I am looking at?
Thanks for your help!

6

The easiest way is to put it on Dropbox or something similar and post the link.

7

https://www.dropbox.com/s/i9a0uyekdrav0f9/3helixsquare_multimodel-outfile.pdb?dl=0

This is a DNA structure, which displays nicely in UCSF chimera but not in Avogadro - it is a 3 helix bundle with strands running between helices – There should be one continuous strand running through the entire structure, supported by a number of shorter ones.
Thanks