[PyMOL] Optimize Geometry {rpblem

2015-07-10 Thread Stephen P. Molnar 
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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Re: [PyMOL] Optimize Geometry {rpblem

2015-07-10 Thread Osvaldo Martin 
I Stephen

I am confused, the problem is with Avogadro, or with the PyMOL's optimize
plugin http://www.pymolwiki.org/index.php/Optimize? I tried to replicate
the problem (with the plugin) and I get the correct answer (the chair
conformation)

Cheers,

Osvaldo


On Fri, Jul 10, 2015 at 11:04 AM, Stephen P. Molnar s.mol...@sbcglobal.net
wrote:

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



 --
 Don't Limit Your Business. Reach for the Cloud.
 GigeNET's Cloud Solutions provide you with the tools and support that
 you need to offload your IT needs and focus on growing your business.
 Configured For All Businesses. Start Your Cloud Today.
 https://www.gigenetcloud.com/
 ___
 PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
 Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
 Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

​
--
Don't Limit Your Business. Reach for the Cloud.
GigeNET's Cloud Solutions provide you with the tools and support that
you need to offload your IT needs and focus on growing your business.
Configured For All Businesses. Start Your Cloud Today.
https://www.gigenetcloud.com/___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net