VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Dec 19 2005 - 17:13:10 CST

Vlad,
  I don't have grace 5.99 here, but try this:
edit the file /usr/local/lib/vmd/scripts/vmd/graphlabels.tcl
and change the line:
    set rc [catch {exec xmgrace -pipe << $input &} msg]
to
    set rc [catch {exec xmgrace -dpipe 0 << $input &} msg]

There's also that "-source" option, but maybe you won't need that.
Give that a try and let me know if it fixes the problem for you
or not.

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Dec 16, 2005 at 04:24:58PM +0100, Vlad Cojocaru wrote:
> Dear vmd users,
>
> I ran into problems trying to view the graphic of a bond distance
> over time using the Label-Graph option in vmd Graphics menu. It looks
> like vmd is trying to access xmgrace via an unknown grace option (see
> error below). I have Grace 5.99.0 installed on my system. I suppose
> that this is due to inconsistencies between vmd and newer versions of
> Grace. Is there a way to fix this?
>
> I tested both vmd 1.8.3 and vmd 1.8.4a22
> Best
> vlad
>
>
> No option -pipe
> Usage of xmgrace command line arguments:
> -autoscale [x|y|xy|none] Set autoscale type
> -barebones Turn off all toolbars
> -block [block_data] Assume data file is block data
> -bxy [x:y:etc.] Form a set from the current block
> data set
> using the current set type from
> columns
> given in the argument
> -datehint [iso|european|us
> |days|seconds|nohint] Set the hint for dates analysis
> (it is only a hint for the parser)
> -dpipe [descriptor] Read data from descriptor on startup
> -fixed [width] [height] Set canvas size fixed to width*height
> -free Use free page layout
> -hardcopy No interactive session, just print and
> quit
> -hdevice [hardcopy_device_name] Set default hardcopy device
> -hdevice-options [option_string] Set options for default hardcopy
> device
> -install Install private colormap
> -noask Assume the answer is yes to all
> requests -
> if the operation would overwrite
> a file,
> grace will do so without prompting
> -noinstall Don't use private colormap
> -noprint In batch mode, do not print
> -nosafe Disable safe mode
> -nosigcatch Don't catch signals
> -npipe [file] Read data from named pipe on startup
> -nxy [nxy_file] Assume data file is in X Y1 Y2 Y3 ...
> format
> -printfile [file for hardcopy output] Save print output to file
> -results [results_file] Write results of some data
> manipulations
> to results_file
> -safe Safe mode (default)
> -saveall [save_file] Save all to save_file
> -seed [seed_value] Integer seed for random number
> generator
> -source [disk|pipe] Source type of next data file
> -timer [delay] Set allowed time slice for real time
> inputs to delay ms
> -settype [xy|xydx|...] Set the type of the next data file
> -version Show the program version
> -wd [directory] Set the working directory
> -usage|-help This message
>
> ** If it scrolls too fast, run `xmgrace -help | more' **
>
> --
>
>
> Dr. Vlad Cojocaru
> EML Research gGmbH
> Molecular and Cellular Modeling Group
> Villa Bosch
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg
> Germany
> Phone: +49-6221-533266
> Fax: +49-6221-533298
> e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
> <mailto:Vlad.Cojocaru_at_eml-r.villa-bosch.de>
> Additional info: my home page
> <http://projects.villa-bosch.de/mcm/people/cojocaru/>
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078