VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 01 2020 - 00:42:28 CDT

Hi,
  There were a number of bugs the very early revs of the VMD
mmCIF/PDBx plugin that have subsequently been fixed that may
explain the crash you have encountered. Thanks for reporting
this. I'll see about adding this as a test case with the current
version and make sure this is fixed in the current rev.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 30, 2020 at 03:42:05PM -0400, Mortimer Hemmit wrote:
> Hello,
>
> Problem: VMD crashes when loading in a Chemical Component Dictionary
> CIF. (The file is in PDBx/mmCIF format which is why I expect it to
> load).
>
> To reproduce (I am using 32-bit VMD noCUDA on a 64-bit Windows 10 machine):
> 1. Download a CIF definition from the PDB. I used ethanol, located at
> https://www.rcsb.org/ligand/EOH
> 2. Load the file into VMD
> 3. VMD crashes and all 3 windows vanish from the screen
>
> Output before it crashes:
> Info) VMD for WIN32, version 1.9.3 (November 30, 2016)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 4 CPUs detected.
> Info) Free system memory: 2047MB (100%)
> Info) OpenGL renderer: AMD Radeon(TM) R5 Graphics
> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVFGS)
> Info) Full GLSL rendering mode is available.
> Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture (8)
> Info) Spaceball driver not installed. Spaceball interface disabled.
> Info) No joysticks found. Joystick interface disabled.
> Info) Dynamically loaded 75 plugins in directory:
> Info) C:/Program Files (x86)/University of Illinois/VMD/plugins/WIN32/molfile
> vmd > pdbxplugin) Could not get atom number
>
> Thank you,
> Mortimer 

-- 
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/