VMD-L Mailing List

From: Arham Amouie (erham65t_at_REMOVE_yahoo.com)
Date: Wed Apr 26 2017 - 11:17:55 CDT

I see. Thank you for your time.

      From: John Stone <johns_at_ks.uiuc.edu>
 To: Arham Amouie <erham65t_at_yahoo.com>
Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
 Sent: Wednesday, April 26, 2017 8:22 PM
 Subject: Re: vmd-l: Bug in VMD 1.9.3?
   
Hi,
  The VTF plugin compilations we've done don't have any of the
optional extra features enabled. 

Looking at the source code for vtfplugin, I see that there are #ifdef
conditional compilation checks for _USE_TCL and _USE_ZLIB, neither of
which are preprocessor defines that would normally be set during
standard VMD compilations, but apparently there are optional features in
the VTF plugin code that are only enabled when it is compiled with
these macros defined.  Olaf never discussed any of that with me, and I
haven't seen any documentation about this anywhere previously, so up to this
point, they have not been defined during any of our VMD compilations of
the VTF plugin.  I'm guessing that those macros are set when the plugin
is compiled as part of the Quantum Espresso source tree, so if you're
using Quantum Espresso, you can probably have VMD load that vtfplugin.so
shared library rather than the standard builds we have provided.

All that being said, you could easily recompile the VTF plugin from source,
enabling these preprocessor macros and thereby enable support for
compressed VTF files and also whatever the Tcl related feature is.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Apr 26, 2017 at 03:37:58PM +0000, Arham Amouie wrote:
>    I have simply used "gzip filename.vtf" to compress it. Once Mr. Olaf Lenz,
>    the author of VTF, told me here that gzip can be used. There is no problem
>    with the uncompressed file.
>    Thank you.
>
>    --------------------------------------------------------------------------
>
>    From: John Stone <johns_at_ks.uiuc.edu>
>    To: Arham Amouie <erham65t_at_yahoo.com>
>    Cc: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>    Sent: Wednesday, April 26, 2017 7:33 PM
>    Subject: Re: vmd-l: Bug in VMD 1.9.3?
>    How is the VTF file compressed?  We need further information about
>    your file to be able to determine if the behavior is unexpect or not.
>
>    Cheers,
>      John Stone
>      [1]vmd_at_ks.uiuc.edu
>    On Wed, Apr 26, 2017 at 12:07:20PM +0000, Arham Amouie wrote:
>    >    Hello. When I try to open a compressed VTF file with pre-compiled
>    VMD,
>    >    this error occurs: "Segmentation fault (core dumped)". Is it a bug?
>    If so,
>    >    where should I report? Thanks.
>    >    Arham
>
>    --
>    NIH Center for Macromolecular Modeling and Bioinformatics
>    Beckman Institute for Advanced Science and Technology
>    University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>    [2]http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
>    [3]http://www.ks.uiuc.edu/Research/vmd/
>
>
> References
>
>    Visible links
>    1. mailto:vmd_at_ks.uiuc.edu
>    2. http://www.ks.uiuc.edu/~johns/
>    3. http://www.ks.uiuc.edu/Research/vmd/ 

-- 
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/