!genprism and !genbox errors

Hello,

In slowly working my way through the tutorials, I've encountered !genbox and
!genprism, both of which don't seem to be working for me. For instance in
"tutorial 1" from "R.W.R." (I assume by now we know what book that is)

!genprism brown_satin_paint stool_leg_sw 4 \
-0.7 -0.7 -0.6 -0.7 -0.6 -0.6 -0.7 -0.6 -1 0 0 2.5

describes a stool leg. However when "oconv"-ing stool_1.rad, I get:

oconv: warning - (!genprism brown_satin_paint stool_leg_sw \
4 -0.7 0.7 -0.7 0.6 -0.6 0.6 -0.6 0.7 -1 0 0 2.5): empty file
nick@nick-desktop:~/scene1$ rvu -vu 0 0 1 -vd 0 1 0 -vp 0 -10 2 -av 1 1 1
stool_1.oct
Usage: genprism material name { - | vfile | N v1 v2 .. vN } [-l lvect][-r
radius][-c][-e]
rvu: warning - (!genprism brown_satin_paint stool_leg_sw \
4 -0.7 -0.7 -0.6 -0.7 -0.6 -0.6 -0.7 -0.6 -1 0 0 2.5): empty file
Usage: genprism material name { - | vfile | N v1 v2 .. vN } [-l lvect][-r
radius][-c][-e]

...for each of the 3 stool legs with their respective differences in
coordinates and names.

Has this command changed too? (such as rview to rvu)

Thanks, in advance (as you can never be stumped it seems!)

-Nick Calcagni

Try -l instead of -1 . Lower case "l" is the flag for the extrusion vector.

-Rob

···

On 8/6/08 8:00 PM, "Nick Calcagni" <[email protected]> wrote:

Hello,

In slowly working my way through the tutorials, I've encountered !genbox and !genprism, both of which don't seem to be working for me. For instance in "tutorial 1" from "R.W.R." (I assume by now we know what book that is)

!genprism brown_satin_paint stool_leg_sw 4 \
-0.7 -0.7 -0.6 -0.7 -0.6 -0.6 -0.7 -0.6 -1 0 0 2.5

describes a stool leg. However when "oconv"-ing stool_1.rad, I get:

oconv: warning - (!genprism brown_satin_paint stool_leg_sw \
4 -0.7 0.7 -0.7 0.6 -0.6 0.6 -0.6 0.7 -1 0 0 2.5): empty file
nick@nick-desktop:~/scene1$ rvu -vu 0 0 1 -vd 0 1 0 -vp 0 -10 2 -av 1 1 1 stool_1.oct
Usage: genprism material name { - | vfile | N v1 v2 .. vN } [-l lvect][-r radius][-c][-e]
rvu: warning - (!genprism brown_satin_paint stool_leg_sw \
4 -0.7 -0.7 -0.6 -0.7 -0.6 -0.6 -0.7 -0.6 -1 0 0 2.5): empty file
Usage: genprism material name { - | vfile | N v1 v2 .. vN } [-l lvect][-r radius][-c][-e]

...for each of the 3 stool legs with their respective differences in coordinates and names.

Has this command changed too? (such as rview to rvu)

Thanks, in advance (as you can never be stumped it seems!)

-Nick Calcagni

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.

Actually I start to feel that the fact that a lot of radiance installations are done on Linux those days, but the tools' names do not have a commen prefix or anything that would make it possible to include them unchanged into any distribution, is getting more and more trouble. As a rule, when encountering such problems, try to find out "which" command you actually call, and what it does, by running it seperately, not from inside a scene description.

CU Lars.

Unless you are using the other package, changing your PATH environment variable to call the directory containing the Radiance binaries ahead of others is the simplest and most appropriate resolution to this problem. There is nothing in Unix-land that says commands need to be complete, and the PATH method is adequate to avoid such issues.

-Greg

···

From: "Lars O. Grobe" <[email protected]>
Date: August 7, 2008 4:58:23 AM EDT

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.

Actually I start to feel that the fact that a lot of radiance installations are done on Linux those days, but the tools' names do not have a commen prefix or anything that would make it possible to include them unchanged into any distribution, is getting more and more trouble. As a rule, when encountering such problems, try to find out "which" command you actually call, and what it does, by running it seperately, not from inside a scene description.

CU Lars.

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

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:

:slight_smile: 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

Hello,

It turns out !genprism does work, it was just another input error on my part.
!genbox however doesn't, and !rgenbox too.

Because it's genrbox ...

Learn how to use system tools to find out which files have been installed
by a package. The program dpkg might be your friend here (I haven't used
Debian/Ubuntu/Linux in a while). The official Debian packages differ from
the standard distribution in some minor ways. Plus the tutorials you are
following are outdated in respect to the current version. If you are not familiar
with your operating system you will have a hard time understanding what's
going on.

As a kick-start help here is the list of files installed by the package:

http://packages.debian.org/lenny/i386/radiance/filelist

The directory you posted isn't on my computer. In fact I can't find any files called "readme" at all.

From the above list it's these files you should read:

/usr/share/doc/radiance/NEWS.Debian.gz
/usr/share/doc/radiance/README.Debian
/usr/share/doc/radiance/README.gz
/usr/share/doc/radiance/changelog.Debian.gz
/usr/share/doc/radiance/copyright

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

The last line is telling: the shell can't find the command called 'rgenbox' - in this case
because it doesn't exist.

If you have the 'locate' command installed you can search for the file on your system
(using a database) or use

find / -name rgenbox

to search the whole system for it (might take a while).

...or this with genbox:

:slight_smile: 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 (-:

This app has nothing to do with Radiance but it has the same name and
it was in Debian first. So the Radiance 'genbox' command had to be renamed
which causes all your troubles right now.

Regards,
Thomas

···

On 16 Aug 2008, at 23:42, Nick Calcagni wrote: