Fwd: Re: path error in compiling svn trunk

Totally fine etiquette. Thanks for the output but looks like it’s closing,
not segfaulting so that’s kinda nice. Although not sure why it is doing
that. I just tested on my system and it works fine. Another idea is to
attach the *.pdb files you’re attempting to load. Feel free to CC the list,
it helps kepe track of stuff.

Time for bed.


Donald

Hi Donald,

I don’t know support/development etiquette, whether or not it’s
interesting for the list, and whether this falls under support or
development. …so if you simply reply forward your response to this
to the list I’ll figure it out. :slight_smile:

I’ve double-checked the paths on my BABEL_LIBDIR using tab complete;
at least I know that the directories exists, and full of things like
mopacformat.o mopacformat.lai … the other directory with cmlformat.o

I’ll post the output to screen below

Thanks for the help
-Lance

From the directory where the executable is located, $avogadro 2>&1 |
tee start.log and simply clicking the “Quit” button gives

Found Engine: “Axes” - "Renders x, y and z axes"
Found Engine: “Dynamic Ball and Stick” - "Renders primitives using Balls
(ato
ms) and Sticks (bonds). Includes demonstration of dynamic rendering based on
di
stance from camera"
Found Engine: “Debug Info” - "Renders debug information"
Found Engine: “Label” - "Renders primitive labels"
Found Engine: “VdW Sphere” - "Renders atoms as Van der Waals spheres"
Found Engine: “Stick” - "Renders as Cylinders"
Found Engine: “Wireframe” - “Wireframe rendering”
“autorotatetool.moc”
“clickmeasuretool.moc”
“cmake_install.cmake”
“drawtool.moc”
"libautorotatetool.so"
Found Tool: “AutoRotate” - “Auto Rotation Tool”
"libclickmeasuretool.so"
Found Tool: “ClickMeasure” - “Click to Measure Tool”
"libdrawtool.so"
Found Tool: “Draw” - “Draws Things”
"libmanipulatetool.so"
Found Tool: “Manipulate” - “Manipulation Tool”
"libnavigatetool.so"
Found Tool: “Navigate” - “Navigation Tool”
"libselectrotatetool.so"
Found Tool: “Select/Rotate” - “Selection and Rotation Tool”
“Makefile”
“manipulatetool.moc”
“navigatetool.moc”
“periodictabledialog.moc”
“qrc_draw.cxx”
“qrc_manipulate.cxx”
“qrc_measure.cxx”
“qrc_navigate.cxx”
“qrc_select.cxx”
“selectrotatetool.moc”
"ui_periodictabledialog.h"
SearchPath: “/home/[[user]]/avogadro/avogadro/build/avogadro/src/extensions”

Found Extension: “GAMESS” - "GAMESS Input Deck Generator"
ForceFieldDialog::ForceFieldDialog()

Found Extension: “Ghemical” - "Ghemical Plugin"
Found Extension: “H2Methyl” - "H2Methyl Plugin"
Found Extension: “Hydrogens” - "Hydrogens Plugin"
Found Extension: “SMARTS” - "SMARTS Plugin"
Found Extension: “UnitCell” - "Unit Cell Parameters Plugin"
close Event

On 7/24/07, Donald Ephraim Curtis d@milkbox.net wrote:

If you’re getting a crash when you try to open a file, I would guess that
it’s
probably something related to your environment variables; (possibly
BABEL_LIBDIR) so please double check that. You seem like you’ve figured
most
of it out so i wouldn’t figure you missed something like that but it’s
discerning why you’re getting that crash when you try to open a file so lets
get to the bottom of it.


Donald

On Tuesday 24 July 2007 03:15:50 am L Philosophy wrote:

Apologies if you already know this–I’m very new at contributing. …
and svn … But Avogadro is too compelling for me to not try it.

http://avogadro.sourceforge.net/wiki/Compiling
The beginner in me stumbled a bit over two points in the wiki:

  1. the svn directory is assumed. The fix:
    $mkdir ~/svn
    $cd ~/svn

Actually, I installed in ~/avogadro because I’m not likely to use it
ever again, and very likely to forget why it’s in my home directory.
I changed the appropriate paths in all following steps

  1. path for eigen in (avogadro-dir)/build/make fails. “no
    eigen/vector.h” seems that the eigen subdir (exists for standard
    eigen install, but not the SVN make) The fix:
    $cd (eigen-dir)/src
    $mkdir eigen
    $cp * eigen/.

make succeeds, Avogadro opens and looks promising, but locks up when I
ask it to open a file, (or give a *.pdb file as command line argument)
but… it runs initially, and that’s relative progress :slight_smile:

Fedora 7, 2.6.22.1-27.fc7, gnome, nvidia drivers

-Lance


This SF.net email is sponsored by: Splunk Inc.
Still grepping through log files to find problems? Stop.
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Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

Hi Donald,

I don’t know support/development etiquette, whether or not it’s
interesting for the list, and whether this falls under support or
development. …so if you simply reply forward your response to this
to the list I’ll figure it out. :slight_smile:

I’ve double-checked the paths on my BABEL_LIBDIR using tab complete;
at least I know that the directories exists, and full of things like
mopacformat.o mopacformat.lai … the other directory with cmlformat.o

I’ll post the output to screen below

Thanks for the help
-Lance

From the directory where the executable is located, $avogadro 2>&1 |
tee start.log and simply clicking the “Quit” button gives

Found Engine: “Axes” - "Renders x, y and z axes"
Found Engine: “Dynamic Ball and Stick” - "Renders primitives using Balls
(ato
ms) and Sticks (bonds). Includes demonstration of dynamic rendering based on
di
stance from camera"
Found Engine: “Debug Info” - "Renders debug information"
Found Engine: “Label” - "Renders primitive labels"
Found Engine: “VdW Sphere” - "Renders atoms as Van der Waals spheres"
Found Engine: “Stick” - "Renders as Cylinders"
Found Engine: “Wireframe” - “Wireframe rendering”
“autorotatetool.moc”
“clickmeasuretool.moc”
“cmake_install.cmake”
“drawtool.moc”
"libautorotatetool.so"
Found Tool: “AutoRotate” - “Auto Rotation Tool”
"libclickmeasuretool.so"
Found Tool: “ClickMeasure” - “Click to Measure Tool”
"libdrawtool.so"
Found Tool: “Draw” - “Draws Things”
"libmanipulatetool.so"
Found Tool: “Manipulate” - “Manipulation Tool”
"libnavigatetool.so"
Found Tool: “Navigate” - “Navigation Tool”
"libselectrotatetool.so"
Found Tool: “Select/Rotate” - “Selection and Rotation Tool”
“Makefile”
“manipulatetool.moc”
“navigatetool.moc”
“periodictabledialog.moc”
“qrc_draw.cxx”
“qrc_manipulate.cxx”
“qrc_measure.cxx”
“qrc_navigate.cxx”
“qrc_select.cxx”
“selectrotatetool.moc”
"ui_periodictabledialog.h"
SearchPath: “/home/[[user]]/avogadro/avogadro/build/avogadro/src/extensions”

Found Extension: “GAMESS” - "GAMESS Input Deck Generator"
ForceFieldDialog::ForceFieldDialog()

Found Extension: “Ghemical” - "Ghemical Plugin"
Found Extension: “H2Methyl” - "H2Methyl Plugin"
Found Extension: “Hydrogens” - "Hydrogens Plugin"
Found Extension: “SMARTS” - "SMARTS Plugin"
Found Extension: “UnitCell” - "Unit Cell Parameters Plugin"
close Event

On 7/24/07, Donald Ephraim Curtis d@milkbox.net wrote:

If you’re getting a crash when you try to open a file, I would guess that
it’s
probably something related to your environment variables; (possibly
BABEL_LIBDIR) so please double check that. You seem like you’ve figured
most
of it out so i wouldn’t figure you missed something like that but it’s
discerning why you’re getting that crash when you try to open a file so lets
get to the bottom of it.


Donald

On Tuesday 24 July 2007 03:15:50 am L Philosophy wrote:

Apologies if you already know this–I’m very new at contributing. …
and svn … But Avogadro is too compelling for me to not try it.

http://avogadro.sourceforge.net/wiki/Compiling
The beginner in me stumbled a bit over two points in the wiki:

  1. the svn directory is assumed. The fix:
    $mkdir ~/svn
    $cd ~/svn

Actually, I installed in ~/avogadro because I’m not likely to use it
ever again, and very likely to forget why it’s in my home directory.
I changed the appropriate paths in all following steps

  1. path for eigen in (avogadro-dir)/build/make fails. “no
    eigen/vector.h” seems that the eigen subdir (exists for standard
    eigen install, but not the SVN make) The fix:
    $cd (eigen-dir)/src
    $mkdir eigen
    $cp * eigen/.

make succeeds, Avogadro opens and looks promising, but locks up when I
ask it to open a file, (or give a *.pdb file as command line argument)
but… it runs initially, and that’s relative progress :slight_smile:

Fedora 7, 2.6.22.1-27.fc7, gnome, nvidia drivers

-Lance


This SF.net email is sponsored by: Splunk Inc.
Still grepping through log files to find problems? Stop.
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Download your FREE copy of Splunk now >> http://get.splunk.com/


Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

Also, are you able to draw / rotate without loading a file?

On Tuesday 24 July 2007 04:01:12 am Donald Ephraim Curtis wrote:

Totally fine etiquette. Thanks for the output but looks like it’s closing,
not segfaulting so that’s kinda nice. Although not sure why it is doing
that. I just tested on my system and it works fine. Another idea is to
attach the *.pdb files you’re attempting to load. Feel free to CC the
list, it helps kepe track of stuff.

Time for bed.


Donald

Hi Donald,

I don’t know support/development etiquette, whether or not it’s
interesting for the list, and whether this falls under support or
development. …so if you simply reply forward your response to this
to the list I’ll figure it out. :slight_smile:

I’ve double-checked the paths on my BABEL_LIBDIR using tab complete;
at least I know that the directories exists, and full of things like
mopacformat.o mopacformat.lai … the other directory with cmlformat.o

I’ll post the output to screen below

Thanks for the help
-Lance

From the directory where the executable is located, $avogadro 2>&1 |
tee start.log and simply clicking the “Quit” button gives

Found Engine: “Axes” - "Renders x, y and z axes"
Found Engine: “Dynamic Ball and Stick” - "Renders primitives using Balls
(ato
ms) and Sticks (bonds). Includes demonstration of dynamic rendering based
on di
stance from camera"
Found Engine: “Debug Info” - "Renders debug information"
Found Engine: “Label” - "Renders primitive labels"
Found Engine: “VdW Sphere” - "Renders atoms as Van der Waals spheres"
Found Engine: “Stick” - "Renders as Cylinders"
Found Engine: “Wireframe” - “Wireframe rendering”
“autorotatetool.moc”
“clickmeasuretool.moc”
“cmake_install.cmake”
“drawtool.moc”
"libautorotatetool.so"
Found Tool: “AutoRotate” - “Auto Rotation Tool”
"libclickmeasuretool.so"
Found Tool: “ClickMeasure” - “Click to Measure Tool”
"libdrawtool.so"
Found Tool: “Draw” - “Draws Things”
"libmanipulatetool.so"
Found Tool: “Manipulate” - “Manipulation Tool”
"libnavigatetool.so"
Found Tool: “Navigate” - “Navigation Tool”
“libselectrotatetool.so"
Found Tool: “Select/Rotate” - “Selection and Rotation Tool”
“Makefile”
“manipulatetool.moc”
“navigatetool.moc”
“periodictabledialog.moc”
“qrc_draw.cxx”
“qrc_manipulate.cxx”
“qrc_measure.cxx”
“qrc_navigate.cxx”
“qrc_select.cxx”
“selectrotatetool.moc”
“ui_periodictabledialog.h"
SearchPath:
”/home/[[user]]/avogadro/avogadro/build/avogadro/src/extensions”

Found Extension: “GAMESS” - "GAMESS Input Deck Generator"
ForceFieldDialog::ForceFieldDialog()

Found Extension: “Ghemical” - "Ghemical Plugin"
Found Extension: “H2Methyl” - "H2Methyl Plugin"
Found Extension: “Hydrogens” - "Hydrogens Plugin"
Found Extension: “SMARTS” - "SMARTS Plugin"
Found Extension: “UnitCell” - "Unit Cell Parameters Plugin"
close Event

On 7/24/07, Donald Ephraim Curtis d@milkbox.net wrote:

If you’re getting a crash when you try to open a file, I would guess that

it’s

probably something related to your environment variables; (possibly
BABEL_LIBDIR) so please double check that. You seem like you’ve figured

most

of it out so i wouldn’t figure you missed something like that but it’s
discerning why you’re getting that crash when you try to open a file so
lets get to the bottom of it.


Donald

On Tuesday 24 July 2007 03:15:50 am L Philosophy wrote:

Apologies if you already know this–I’m very new at contributing. …
and svn … But Avogadro is too compelling for me to not try it.

http://avogadro.sourceforge.net/wiki/Compiling
The beginner in me stumbled a bit over two points in the wiki:

  1. the svn directory is assumed. The fix:
    $mkdir ~/svn
    $cd ~/svn

Actually, I installed in ~/avogadro because I’m not likely to use it
ever again, and very likely to forget why it’s in my home directory.
I changed the appropriate paths in all following steps

  1. path for eigen in (avogadro-dir)/build/make fails. “no
    eigen/vector.h” seems that the eigen subdir (exists for standard
    eigen install, but not the SVN make) The fix:
    $cd (eigen-dir)/src
    $mkdir eigen
    $cp * eigen/.

make succeeds, Avogadro opens and looks promising, but locks up when I
ask it to open a file, (or give a *.pdb file as command line argument)
but… it runs initially, and that’s relative progress :slight_smile:

Fedora 7, 2.6.22.1-27.fc7, gnome, nvidia drivers

-Lance


– This SF.net email is sponsored by: Splunk Inc.
Still grepping through log files to find problems? Stop.
Now Search log events and configuration files using AJAX and a browser.
Download your FREE copy of Splunk now >> http://get.splunk.com/


Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

Hi Donald,

I don’t know support/development etiquette, whether or not it’s
interesting for the list, and whether this falls under support or
development. …so if you simply reply forward your response to this
to the list I’ll figure it out. :slight_smile:

I’ve double-checked the paths on my BABEL_LIBDIR using tab complete;
at least I know that the directories exists, and full of things like
mopacformat.o mopacformat.lai … the other directory with cmlformat.o

I’ll post the output to screen below

Thanks for the help
-Lance

From the directory where the executable is located, $avogadro 2>&1 |
tee start.log and simply clicking the “Quit” button gives

Found Engine: “Axes” - "Renders x, y and z axes"
Found Engine: “Dynamic Ball and Stick” - "Renders primitives using Balls
(ato
ms) and Sticks (bonds). Includes demonstration of dynamic rendering based
on di
stance from camera"
Found Engine: “Debug Info” - "Renders debug information"
Found Engine: “Label” - "Renders primitive labels"
Found Engine: “VdW Sphere” - "Renders atoms as Van der Waals spheres"
Found Engine: “Stick” - "Renders as Cylinders"
Found Engine: “Wireframe” - “Wireframe rendering”
“autorotatetool.moc”
“clickmeasuretool.moc”
“cmake_install.cmake”
“drawtool.moc”
"libautorotatetool.so"
Found Tool: “AutoRotate” - “Auto Rotation Tool”
"libclickmeasuretool.so"
Found Tool: “ClickMeasure” - “Click to Measure Tool”
"libdrawtool.so"
Found Tool: “Draw” - “Draws Things”
"libmanipulatetool.so"
Found Tool: “Manipulate” - “Manipulation Tool”
"libnavigatetool.so"
Found Tool: “Navigate” - “Navigation Tool”
“libselectrotatetool.so"
Found Tool: “Select/Rotate” - “Selection and Rotation Tool”
“Makefile”
“manipulatetool.moc”
“navigatetool.moc”
“periodictabledialog.moc”
“qrc_draw.cxx”
“qrc_manipulate.cxx”
“qrc_measure.cxx”
“qrc_navigate.cxx”
“qrc_select.cxx”
“selectrotatetool.moc”
“ui_periodictabledialog.h"
SearchPath:
”/home/[[user]]/avogadro/avogadro/build/avogadro/src/extensions”

Found Extension: “GAMESS” - "GAMESS Input Deck Generator"
ForceFieldDialog::ForceFieldDialog()

Found Extension: “Ghemical” - "Ghemical Plugin"
Found Extension: “H2Methyl” - "H2Methyl Plugin"
Found Extension: “Hydrogens” - "Hydrogens Plugin"
Found Extension: “SMARTS” - "SMARTS Plugin"
Found Extension: “UnitCell” - "Unit Cell Parameters Plugin"
close Event

On 7/24/07, Donald Ephraim Curtis d@milkbox.net wrote:

If you’re getting a crash when you try to open a file, I would guess that

it’s

probably something related to your environment variables; (possibly
BABEL_LIBDIR) so please double check that. You seem like you’ve figured

most

of it out so i wouldn’t figure you missed something like that but it’s
discerning why you’re getting that crash when you try to open a file so
lets get to the bottom of it.


Donald

On Tuesday 24 July 2007 03:15:50 am L Philosophy wrote:

Apologies if you already know this–I’m very new at contributing. …
and svn … But Avogadro is too compelling for me to not try it.

http://avogadro.sourceforge.net/wiki/Compiling
The beginner in me stumbled a bit over two points in the wiki:

  1. the svn directory is assumed. The fix:
    $mkdir ~/svn
    $cd ~/svn

Actually, I installed in ~/avogadro because I’m not likely to use it
ever again, and very likely to forget why it’s in my home directory.
I changed the appropriate paths in all following steps

  1. path for eigen in (avogadro-dir)/build/make fails. “no
    eigen/vector.h” seems that the eigen subdir (exists for standard
    eigen install, but not the SVN make) The fix:
    $cd (eigen-dir)/src
    $mkdir eigen
    $cp * eigen/.

make succeeds, Avogadro opens and looks promising, but locks up when I
ask it to open a file, (or give a *.pdb file as command line argument)
but… it runs initially, and that’s relative progress :slight_smile:

Fedora 7, 2.6.22.1-27.fc7, gnome, nvidia drivers

-Lance


– This SF.net email is sponsored by: Splunk Inc.
Still grepping through log files to find problems? Stop.
Now Search log events and configuration files using AJAX and a browser.
Download your FREE copy of Splunk now >> http://get.splunk.com/


Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

I was just playing with it more, and yes I can draw and rotate to some
extent. I’m not familiar with the commands, but there appears to be
some graphics corruption part way through the draw. For example a
blue selected bond would appear without other atoms drawn, when
rotated it would be obscured by said previously drawn atoms.
Eventually I hit “quit” again, a “save this file?” dialog appeared,
and when I tried to save it froze on the “Save Moledule As” dialog.
The hang on opening a file occurs at the same stage. However there’s
different behavior if I feed a *pdb while opening from the command
line: no Avogadro window spawns after the terminal messages (below)

-Lance (in Japan–has an excuse for being up so “late”)

On 7/24/07, Donald E wrote:

Also, are you able to draw / rotate without loading a file?

On Tuesday 24 July 2007 04:01:12 am Donald Ephraim Curtis wrote:

Totally fine etiquette. Thanks for the output but looks like it’s closing,
not segfaulting so that’s kinda nice. Although not sure why it is doing
that. I just tested on my system and it works fine. Another idea is to
attach the *.pdb files you’re attempting to load. Feel free to CC the
list, it helps kepe track of stuff.

Time for bed.


Donald

Hi Donald,

I don’t know support/development etiquette, whether or not it’s
interesting for the list, and whether this falls under support or
development. …so if you simply reply forward your response to this
to the list I’ll figure it out. :slight_smile:

I’ve double-checked the paths on my BABEL_LIBDIR using tab complete;
at least I know that the directories exists, and full of things like
mopacformat.o mopacformat.lai … the other directory with cmlformat.o

I’ll post the output to screen below

Thanks for the help
-Lance

From the directory where the executable is located, $avogadro 2>&1 |
tee start.log and simply clicking the “Quit” button gives

Found Engine: “Axes” - "Renders x, y and z axes"
Found Engine: “Dynamic Ball and Stick” - "Renders primitives using Balls
(ato
ms) and Sticks (bonds). Includes demonstration of dynamic rendering based
on di
stance from camera"
Found Engine: “Debug Info” - "Renders debug information"
Found Engine: “Label” - "Renders primitive labels"
Found Engine: “VdW Sphere” - "Renders atoms as Van der Waals spheres"
Found Engine: “Stick” - "Renders as Cylinders"
Found Engine: “Wireframe” - “Wireframe rendering”
“autorotatetool.moc”
“clickmeasuretool.moc”
“cmake_install.cmake”
“drawtool.moc”
"libautorotatetool.so"
Found Tool: “AutoRotate” - “Auto Rotation Tool”
"libclickmeasuretool.so"
Found Tool: “ClickMeasure” - “Click to Measure Tool”
"libdrawtool.so"
Found Tool: “Draw” - “Draws Things”
"libmanipulatetool.so"
Found Tool: “Manipulate” - “Manipulation Tool”
"libnavigatetool.so"
Found Tool: “Navigate” - “Navigation Tool”
“libselectrotatetool.so"
Found Tool: “Select/Rotate” - “Selection and Rotation Tool”
“Makefile”
“manipulatetool.moc”
“navigatetool.moc”
“periodictabledialog.moc”
“qrc_draw.cxx”
“qrc_manipulate.cxx”
“qrc_measure.cxx”
“qrc_navigate.cxx”
“qrc_select.cxx”
“selectrotatetool.moc”
“ui_periodictabledialog.h"
SearchPath:
”/home/[[user]]/avogadro/avogadro/build/avogadro/src/extensions”

Found Extension: “GAMESS” - "GAMESS Input Deck Generator"
ForceFieldDialog::ForceFieldDialog()

Found Extension: “Ghemical” - "Ghemical Plugin"
Found Extension: “H2Methyl” - "H2Methyl Plugin"
Found Extension: “Hydrogens” - "Hydrogens Plugin"
Found Extension: “SMARTS” - "SMARTS Plugin"
Found Extension: “UnitCell” - "Unit Cell Parameters Plugin"
close Event

On 7/24/07, Donald wrote:

If you’re getting a crash when you try to open a file, I would guess that

it’s

probably something related to your environment variables; (possibly
BABEL_LIBDIR) so please double check that. You seem like you’ve figured

most

of it out so i wouldn’t figure you missed something like that but it’s
discerning why you’re getting that crash when you try to open a file so
lets get to the bottom of it.


Donald

On Tuesday 24 July 2007 03:15:50 am L Philosophy wrote:

Apologies if you already know this–I’m very new at contributing. …
and svn … But Avogadro is too compelling for me to not try it.

http://avogadro.sourceforge.net/wiki/Compiling
The beginner in me stumbled a bit over two points in the wiki:

  1. the svn directory is assumed. The fix:
    $mkdir ~/svn
    $cd ~/svn

Actually, I installed in ~/avogadro because I’m not likely to use it
ever again, and very likely to forget why it’s in my home directory.
I changed the appropriate paths in all following steps

  1. path for eigen in (avogadro-dir)/build/make fails. “no
    eigen/vector.h” seems that the eigen subdir (exists for standard
    eigen install, but not the SVN make) The fix:
    $cd (eigen-dir)/src
    $mkdir eigen
    $cp * eigen/.

make succeeds, Avogadro opens and looks promising, but locks up when I
ask it to open a file, (or give a *.pdb file as command line argument)
but… it runs initially, and that’s relative progress :slight_smile:

Fedora 7, 2.6.22.1-27.fc7, gnome, nvidia drivers

-Lance


– This SF.net email is sponsored by: Splunk Inc.
Still grepping through log files to find problems? Stop.
Now Search log events and configuration files using AJAX and a browser.
Download your FREE copy of Splunk now >> http://get.splunk.com/


Avogadro-devel mailing list
Avogadro-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/avogadro-devel

Hi Donald,

I don’t know support/development etiquette, whether or not it’s
interesting for the list, and whether this falls under support or
development. …so if you simply reply forward your response to this
to the list I’ll figure it out. :slight_smile:

I’ve double-checked the paths on my BABEL_LIBDIR using tab complete;
at least I know that the directories exists, and full of things like
mopacformat.o mopacformat.lai … the other directory with cmlformat.o

I’ll post the output to screen below

Thanks for the help
-Lance

From the directory where the executable is located, $avogadro 2>&1 |
tee start.log and simply clicking the “Quit” button gives

Found Engine: “Axes” - "Renders x, y and z axes"
Found Engine: “Dynamic Ball and Stick” - "Renders primitives using Balls
(ato
ms) and Sticks (bonds). Includes demonstration of dynamic rendering based
on di
stance from camera"
Found Engine: “Debug Info” - "Renders debug information"
Found Engine: “Label” - "Renders primitive labels"
Found Engine: “VdW Sphere” - "Renders atoms as Van der Waals spheres"
Found Engine: “Stick” - "Renders as Cylinders"
Found Engine: “Wireframe” - “Wireframe rendering”
“autorotatetool.moc”
“clickmeasuretool.moc”
“cmake_install.cmake”
“drawtool.moc”
"libautorotatetool.so"
Found Tool: “AutoRotate” - “Auto Rotation Tool”
"libclickmeasuretool.so"
Found Tool: “ClickMeasure” - “Click to Measure Tool”
"libdrawtool.so"
Found Tool: “Draw” - “Draws Things”
"libmanipulatetool.so"
Found Tool: “Manipulate” - “Manipulation Tool”
"libnavigatetool.so"
Found Tool: “Navigate” - “Navigation Tool”
“libselectrotatetool.so"
Found Tool: “Select/Rotate” - “Selection and Rotation Tool”
“Makefile”
“manipulatetool.moc”
“navigatetool.moc”
“periodictabledialog.moc”
“qrc_draw.cxx”
“qrc_manipulate.cxx”
“qrc_measure.cxx”
“qrc_navigate.cxx”
“qrc_select.cxx”
“selectrotatetool.moc”
“ui_periodictabledialog.h"
SearchPath:
”/home/[[user]]/avogadro/avogadro/build/avogadro/src/extensions”

Found Extension: “GAMESS” - "GAMESS Input Deck Generator"
ForceFieldDialog::ForceFieldDialog()

Found Extension: “Ghemical” - "Ghemical Plugin"
Found Extension: “H2Methyl” - "H2Methyl Plugin"
Found Extension: “Hydrogens” - "Hydrogens Plugin"
Found Extension: “SMARTS” - "SMARTS Plugin"
Found Extension: “UnitCell” - "Unit Cell Parameters Plugin"
close Event

On 7/24/07, Donald Ephraim Curtis d@milkbox.net wrote:

If you’re getting a crash when you try to open a file, I would guess that

it’s

probably something related to your environment variables; (possibly
BABEL_LIBDIR) so please double check that. You seem like you’ve figured

most

of it out so i wouldn’t figure you missed something like that but it’s
discerning why you’re getting that crash when you try to open a file so
lets get to the bottom of it.


Donald

On Tuesday 24 July 2007 03:15:50 am L Philosophy wrote:

Apologies if you already know this–I’m very new at contributing. …
and svn … But Avogadro is too compelling for me to not try it.

http://avogadro.sourceforge.net/wiki/Compiling
The beginner in me stumbled a bit over two points in the wiki:

  1. the svn directory is assumed. The fix:
    $mkdir ~/svn
    $cd ~/svn

Actually, I installed in ~/avogadro because I’m not likely to use it
ever again, and very likely to forget why it’s in my home directory.
I changed the appropriate paths in all following steps

  1. path for eigen in (avogadro-dir)/build/make fails. “no
    eigen/vector.h” seems that the eigen subdir (exists for standard
    eigen install, but not the SVN make) The fix:
    $cd (eigen-dir)/src
    $mkdir eigen
    $cp * eigen/.

make succeeds, Avogadro opens and looks promising, but locks up when I
ask it to open a file, (or give a *.pdb file as command line argument)
but… it runs initially, and that’s relative progress :slight_smile:

Fedora 7, 2.6.22.1-27.fc7, gnome, nvidia drivers

-Lance


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Avogadro-devel@lists.sourceforge.net
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[[I tried to read a reply on the sourceforge.net archive page, but it seemed the forwarding arrows got corrupted. Couldn’t see anything I hadn’t already seen.]]

Update: Avogadro correctly loads some of my *.pdb files, when started
from the command line. It can also rotate them. However, it hangs on
the files I really want to open (more on that below), and it still
hangs on the “open file” dialog. I’ll attach some screen shots.
Also, once I tried selecting an atom besides Carbon, but after opening
the atom selector dialog it froze GNOME. (I was able to kill the
process via Ctrl-Alt-F1 terminal.) I suspect the conflict is graphics
related. I use kmod-nvidia-100.14.11-1.2.6.22.1_27.fc7, the hardware
is nVidia Quadro FX 550 128mb I think, screen is 1920x1200, in gnome.

About my *pdb files: I have general interest in a useful program like
Avogadro, but I also was hoping to use it as a viewer for an unrelated
project. I want to view XYZ grid points as 3D spheres. Currently I
convert straight forward 3-column integer cubic XYZ files to PDB,
designating each point as an unbonded oxygen waters. … The files get
pretty big, up to 99999 atoms, which I believe is the max for *.pdb
format. (I wish it could do more! Visualizing the location of
elements for the finite element code DDSCAT, up to 500k elements)

Avogadro will open the files, but it takes a very long time for the
Avogadro window to appear the number of atoms is near or greater than
2000. It seems that the closer the atoms are to each other, the lower
that “effective max” becomes. I can view the file in Windows using
the “protein explorer” front-end for MDL Chime, but it’s clunky and
I’d much prefer a native LINUX app. I’m trying out “FirstGlance in
Jmol” today. Any/all advice about a better file-format I should use
(or if you know the application I’m thinking of) would be greatly
appreciated. I’ve attached my “unbonded O atoms” *.pdb as well.

I don’t expect Avogadro was meant to be a protein viewer, so I
understand if my intended application will simply never work. But for
now I’m happy to help track down the graphics/Qt bug I’m experiencing

-Lance