[Radiance-general] !genprism and !genbox errors

[Nick Calcagni]

Hello,

It turns out !genprism does work, it was just another input error on my
part. !genbox however doesn't, and !rgenbox too. The directory you posted
isn't on my computer. In fact I can't find any files called "readme" at all.

I get many many lines of this with rgenbox:

xform: (standard input): warning - empty file
xform: (!rgenbox   red_tile       tile_a   1 1 .1 -b .025  | xform -t 1 1
-.1): warning - empty file
sh: rgenbox: not found
xform: (standard input): warning - empty file
xform: (!rgenbox   white_tile     tile_a   1 1 .1 -b .025  | xform -t 0 1
-.1): warning - empty file
sh: rgenbox: not found

...or this with genbox:

 :-)  G  R  O  M  A  C  S  (-:

                  Green Red Orange Magenta Azure Cyan Skyblue

                            :-)  VERSION 3.3.3  (-:


      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2008, The GROMACS development team,
            check out http://www.gromacs.org for more information.

         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                                :-)  genbox  (-:

Option     Filename  Type         Description
------------------------------------------------------------
 -cp    protein.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
                                   xml
 -cs     spc216.gro  Input, Opt., Lib. Generic structure: gro g96 pdb tpr
tpb
                                   tpa xml
 -ci     insert.gro  Input, Opt.  Generic structure: gro g96 pdb tpr tpb tpa
                                   xml
  -o        out.gro  Output       Generic structure: gro g96 pdb xml
  -p      topol.top  In/Out, Opt. Topology file

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-[no]X       bool   no      Use dialog box GUI to edit command line options
-nice        int    19      Set the nicelevel
-box         vector 0 0 0   box size
-nmol        int    0       no of extra molecules to insert
-try         int    10      try inserting -nmol*-try times
-seed        int    1997    random generator seed
-vdwd        real   0.105   default vdwaals distance
-shell       real   0       thickness of optional water layer around solute
-maxsol      int    0       maximum number of solvent molecules to add if
                            they fit in the box. If zero (default) this is
                            ignored
-[no]vel     bool   no      keep velocities from input solute and solvent


-------------------------------------------------------
Program genbox, VERSION 3.3.3
Source code file: ../../../../src/gmxlib/statutil.c, line: 797

Invalid command line argument:
red_tile
-------------------------------------------------------

"Take Dehydrated Water On Your Desert Trips" (Space Quest III)

xform: (standard input): warning - empty file
xform: (!genbox   red_tile       tile_a   1 1 .1 -b .025  | xform -t 0 0
-.1): warning - empty file


Could you walk me through what to do, in order to get Radiance's !genbox
working, instead of, what I'm assuming, is another program for
who-knows-what?

Thank you!
Nick


Lars O. Grobe wrote:
>*
*>>* Has this command changed too? (such as rview to rvu)
*>*
*>* On Linux systems, there already exists a command genbox. So the package
*>* maintainers (I guess you use a debian or ubuntu setup?) have to rename
*>* these tools (I would guess to rgenbox, rgenprism) to avoid
*>* unpredicteable behaviour. The source tree at radsite/radiance-online
*>* doesn't reflect these changes, the documentation doesn't do it neither.
*
On Debian and Ubuntu these changes are documented in
/usr/share/doc/radiance/README.Debian
There's also described how to modify $PATH to get the old function back.


Cheers,

Bernd

-- 
 Bernd Zeimetz                           Debian GNU/Linux Developer
 GPG Fingerprint: 06C8 C9A2 EAAD E37E 5B2C BE93 067A AD04 C93B FF79
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