>> Stéphane,
>>It looks like a slash/backslash issue between windows and linux:
>>C:\Program Files (x86)\PyMOL_v13\PyMOL/modules\pymol\parser.py
Thanks Jed,
How to change it, since I can not to modify it with text editor (it seems to be
used by another program, even if pymol is closed
S
--------------------------------------------------------------------
Hi Pymol users
I use Pymol v1.3 on Windows and I would like to use the loadBfacts.py
(http://www.pymolwiki.org/index.php/Load_new_B-factors) (renamed, here,
loadB2Fact.py) to change the B factor value according to other values stored in
an external txt file. On my linux machine, I use the following script that
works well
### Script ##
bg black
hide all
select BENZ, resname BEN
hide BEN
select SOL, resname SOL
hide SOL
select DOP, resname DOP
hide DOP
select protein, resi 1-76
run loadB2Fact.py
loadBfacts protein, 1,
UBQ_TIP4P_Bulk_Water_residue_0.350_nm_Average_Statistics.dat
cartoon automatic, protein
set_view (\
-0.252517521, 0.895963371, 0.365354568,\
0.693045497, 0.430974960, -0.577881873,\
-0.675220251, 0.107282706, -0.729772329,\
-0.000030319, -0.000010751, -106.549461365,\
30.012023926, 31.324144363, 31.591945648,\
66.820175171, 146.280471802, -20.000000000 )
###End Script
But on windows, i obtained the following errors
PyMOL>run ./loadB2Fact.py
Traceback (most recent call last):
File "C:\Program Files (x86)\PyMOL_v13\PyMOL/modules\pymol\parser.py", line
338, in parse
parsing.run_file(path,self.pymol_names,self.pymol_names)
File "C:\Program Files (x86)\PyMOL_v13\PyMOL/modules\pymol\parsing.py", line
455, in run_file
execfile(file,global_ns,local_ns)
IOError: [Errno 2] No such file or directory: './loadB2Fact.py'
PyMOL>loadBfacts protein, 1,
UBQ_TIP4P_Bulk_Water_residue_0.350_nm_Average_Statistics.dat
Traceback (most recent call last):
File "C:\Program Files (x86)\PyMOL_v13\PyMOL/modules\pymol\parser.py", line
464, in parse
exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
File "<string>", line 1
loadBfacts protein, 1,
UBQ_TIP4P_Bulk_Water_residue_0.350_nm_Average_Statistics.dat
^
SyntaxError: invalid syntax
And I see nothing on the screen
Could you help me ?
Thanks
St?phane
------------------------------
Message: 3
Date: Fri, 10 Jul 2015 18:14:41 +0530
From: Gazal <gazal...@gmail.com>
Subject: [PyMOL] How to find RMSD values using fitting.py using Shell
script
To: pymol-users@lists.sourceforge.net
Message-ID:
<CAC-EGRpq9ORP2p7HT9icysLDWQDVnfmem=pfvcn+izijtr+...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Hi,
I'm trying to find the RMSD values for batch purposes. The command which I
found works for the Pymol-command line.
I was hoping if I could get an idea about using the python script
fitting.py in my shell script without triggering the Pymol GUI.
Thanks in advance.
Gazal
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Message: 4
Date: Fri, 10 Jul 2015 10:04:24 -0400
From: "Stephen P. Molnar" <s.mol...@sbcglobal.net>
Subject: [PyMOL] Optimize Geometry {rpblem
To: "pymol-users@lists.sourceforge.net"
<pymol-users@lists.sourceforge.net>
Message-ID: <559fd0e8.8090...@sbcglobal.net>
Content-Type: text/plain; charset="utf-8"
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
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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
------------------------------
Message: 5
Date: Fri, 10 Jul 2015 11:43:19 -0300
From: Osvaldo Martin <aloctavo...@gmail.com>
Subject: Re: [PyMOL] Optimize Geometry {rpblem
To: "Stephen P. Molnar" <s.mol...@sbcglobal.net>
Cc: "pymol-users@lists.sourceforge.net"
<pymol-users@lists.sourceforge.net>
Message-ID:
<cagmh68vs_hi86efhbgkt1bod1xm28bjjjpntysyo8mb9d2n...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
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
>
>
>
> ------------------------------------------------------------------------------
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