VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Dec 19 2005 - 17:24:32 CST

Vlad,
  Thanks for the update. I'm curious if they do plan to change the command
line options for the future revs of Grace, as we'll ultimately want to
support whatever they do in the future stable versions of course.
 
  John

On Tue, Dec 20, 2005 at 12:22:45AM +0100, Cojocaru,Vlad wrote:
>
> John,
> The Grace problem turned out to be a Grace version problem ... It works absolutely fine with Grace 5.1.18 or 5.1.19 ... I had in my office this 5.99.0 which I read afterwards on the Grace website that it is just a test version which they use for the development of grace 6 and they do not recommend the use of 5.99.0 ...After I checked it home with 5.1.18 and I notice that it works fine I asked our system adm to install a stable Grace and that fixed the problem .... So, I think we should not try to adapt to this 5.99.0 version
>
> Best
> vlad
>
> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: Tue 12/20/2005 12:13 AM
> To: Cojocaru,Vlad
> Cc: VMD list
> Subject: Re: vmd-l: vmd and xmgrace
>
> 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
>
>
> 

-- 
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