I have a bit of a strange problem. I have evaluated a number of Linux
distributions in a VMware Player environment on my 64 bit laptop.
I compile PyMol using the attached protocol.
The OS is BioLinux v-8.0.5 with Avogadro Version 1.1.1
Library Version 1.1.1
Open Babel Version 2.3.2
Qt Version 4.8.6
The problem involves the Extensions/Optimize Geometry feature with
cyclohexane as the test molecule. Cyclohexane as built is a planar
molecule, but when I optimize the geometry it remains in a planar
conformation. However in some of my test systems the geometry is
returned as the chair isomer, which, of course, is correct!
I will make the wild assumption (yes, I know how the word can be broken
down) that there is a missing library. Which one might it be? Is any
other information needed in order to address this rather nagging problem?
Thanks in advance.
--
Stephen P. Molnar, Ph.D. Life is a fuzzy set
www.FoundationForChemistry.com Stochastic and multivariate
(614)312-7528 (c)
Skype: smolnar1
sudo apt-get install subversion build-essential python-dev python-pmw
libglew-dev freeglut3-dev libpng-dev libfreetype6-dev libxml2-dev
cd /tmp
svn co svn://svn.code.sf.net/p/pymol/code/trunk/pymol
cd pymol
prefix=/home/comp/Apps/pymol
modules=$prefix/modules
export CPPFLAGS="-std=c++11"
python setup.py build install \
--home=$prefix \
--install-lib=$modules \
--install-scripts=$prefix
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