Fw: Installing Avogadro

General Discussion
1

Hi again,
I cannot view xyz or mol2 files on my Linux install. It works on my
Windows install. Is this an openbabel issue?

I also get some Qstacked errors when launching avogadro, of the kind:

QStackedLayout::setCurrentWidget: Widget 0x2bd42a0 not contained in stack.

Jerry

Gerald J. Tanoury, Ph.D.
Scientific Fellow II
Chemical Development
Vertex Pharmaceuticals Incorporated
130 Waverly Street
Cambridge, MA 02139-4242
ph: (617) 444-6219
fax: (617) 444-6920
jerry_tanoury@vrtx.com

----- Forwarded by Jerry Tanoury/BOS1/VRTX on 08/16/2010 12:21 PM -----

From:
Jerry Tanoury/BOS1/VRTX
To:
Geoffrey Hutchison geoff.hutchison@gmail.com
Cc:
avogadro-discuss@lists.sourceforge.net, support@q-chem.com
Date:
08/16/2010 11:43 AM
Subject:
Re: Installing Avogadro

Hi Geoff,
I used option 2 and got it installed.

Thanks,
Jerry

From:
Geoffrey Hutchison geoff.hutchison@gmail.com
To:
Jerry_Tanoury@vrtx.com
Cc:
support@q-chem.com, avogadro-discuss@lists.sourceforge.net
Date:
08/16/2010 11:04 AM
Subject:
Re: Installing Avogadro

Hi Jerry,

There’s a separate support list for Avogadro at avogadro-discuss (cc’ed on
this message). On principal, I’d also suggest grabbing OB-2.2.3, since it
has quite a few bug fixes.

There are two options for handling this.

  1. The current Avogadro releases use pkg-config to “fall back” when they
    can’t find packages. If you have it, just make sure /cluster/home/tanoury
    is included in the PKG_CONFIG_PATH, e.g.

export
PKG_CONFIG_PATH=/opt/local/lib/pkgconfig:/usr/lib/pkgconfig:/usr/local/lib/pkgconfig:/cluster/home/tanoury/lib/pkgconfig

  1. Make sure to include -DOPENBABEL2_VERSION_MET=true as suggested in the
    wiki build instructions:

http://avogadro.openmolecules.net/wiki/Compiling_on_Linux_and_Mac_OS_X

Hope that helps,
-Geoff

Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

From: Jerry_Tanoury@vrtx.com
Sent: Monday, August 16, 2010 8:22 AM
To: support@q-chem.com
Subject: Installing Avogadro

Hi,
I don’t know if you can help me with installing Avogadro on my Linux
box, but it seems to be the preferred gui for running Q-Chem. The
avogadro install script is having significant trouble finding openbabel.
Here is what has happened:

[tanoury@tanourylnx:build]$ cmake
-DCMAKE_INSTALL_PREFIX=/cluster/home/tanoury
-DEIGEN_INCLUDE_DIR=/cluster/home/tanoury/eigen/Eigen
-DCMAKE_INSTALL_DIR=/cluster/home/tanoury/lib
-DOPENBABEL2_INCLUDE_DIR=/cluster/home/tanoury/include/openbabel-2.0
-DOPENBABEL2_LIBRARIES=/cluster/home/tanoury/lib/openbabel/2.2.2 …/
– The build type is Release
– Found lupdate: /cluster/home/tanoury/Trolltech/Qt-4.5.3/bin/lupdate
– Found lrelease: /cluster/home/tanoury/Trolltech/Qt-4.5.3/bin/lrelease
– Found lconvert: /cluster/home/tanoury/Trolltech/Qt-4.5.3/bin/lconvert
– Found ZLIB: /usr/include
– checking for module ‘openbabel-2.0>=2.2.2’
– package ‘openbabel-2.0>=2.2.2’ not found
CMake Error at cmake/modules/FindOpenBabel2.cmake:81 (message):
Could NOT find OpenBabel 2.2 or later
Call Stack (most recent call first):
CMakeLists.txt:131 (find_package)

– Configuring incomplete, errors occurred!

I have installed Qt-4.5.3, eigen and openbabel. Running “make check”
with openbabel works.

Thanks,
Jerry

2

I also get some Qstacked errors when launching avogadro, of the kind:
QStackedLayout::setCurrentWidget: Widget 0x2bd42a0 not contained in stack.

This is definitely a warning. If I could track down the exact culprit, it would be gone. There’s often comments about PNG issues which also appear, but are irrelevant. (These seem to be Qt verbosity.)

I cannot view xyz or mol2 files on my Linux install. It works on my Windows install. Is this an openbabel issue?

This indicates that Open Babel cannot find its format libraries. On Linux, I’d set the environment variables:

BABEL_LIBDIR=/home/ghutchis/lib/openbabel
BABEL_DATADIR=/home/ghutchis/share/openbabel

(or similar)

Hope that helps,
-Geoff