[PyMOL] How to find RMSD values using fitting.py using Shell script
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 -- 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
[PyMOL] Optimize Geometry {rpblem
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 -- 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
Re: [PyMOL] Optimize Geometry {rpblem
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
Re: [PyMOL] How to find RMSD values using fitting.py using Shell script
Hi Gazal, Generally when I want to do batch operations using PyMOL I wrote a Python script and I call PyMOL from within that script. I prefer this way because I think is more flexible and simple than using PyMOL from the command line. In those cases I start the Python script with the following imports: import *main* *main*.pymol_argv = [‘pymol’,’-qc’] # Pymol: quiet and no GUI import pymol from pymol import cmd, stored pymol.finish_launching() Nevertheless, if you want to call PyMOL from the command line you have several options http://www.pymolwiki.org/index.php/Command_Line_Options that you can pass to PyMOL like “-qc” , i.e. quiet and no GUI Let us know if this answer your question, or if you still have doubts. Cheers, Osvaldo. On Fri, Jul 10, 2015 at 9:44 AM, Gazal gazal...@gmail.com wrote: 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 -- 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
Re: [PyMOL] How to find RMSD values using fitting.py using Shell script
http://www.pymolwiki.org/index.php/Command_Line_Options http://www.pymolwiki.org/index.php/Command_Line_Options see the -c and -r options. I also use -q pymol -qcr script.py — arg1 arg2 arg3 On Jul 10, 2015, at 8:44 AM, Gazal gazal...@gmail.com wrote: 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 -- 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
Re: [PyMOL] Problem with loadBfact.py on windows
This is the problem. Pymol’s working directory is not where you have this file. So, the script never loads. On Jul 10, 2015, at 12:20 PM, ABEL Stephane 175950 stephane.a...@cea.fr wrote: No such file or directory: './loadB2Fact.py' -- 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
[PyMOL] Problem with loadBfact.py on windows
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,\
-0.30319, -0.10751, -106.549461365,\
30.012023926, 31.324144363, 31.591945648,\
66.820175171, 146.280471802, -20.0 )
###End Script
But on windows, i obtained the following errors
PyMOLrun ./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'
PyMOLloadBfacts 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
-- next part --
An HTML attachment was scrubbed...
--
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
-- next part --
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 \
[PyMOL] Problem with loadBfact.py on windows (ABEL Stephane 175950
I have reinstall the program and removed an old version of Pymol. Now the script works Thanks -- Message: 2 Date: Fri, 10 Jul 2015 12:44:40 + From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [PyMOL] Problem with loadBfact.py on windows To: pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net Message-ID: 3e39b768bb199548ab18f7289e7534af1b471...@exdag0-b0.intra.cea.fr Content-Type: text/plain; charset=iso-8859-1 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,\ -0.30319, -0.10751, -106.549461365,\ 30.012023926, 31.324144363, 31.591945648,\ 66.820175171, 146.280471802, -20.0 ) ###End Script But on windows, i obtained the following errors PyMOLrun ./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' PyMOLloadBfacts 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 -- 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
[PyMOL] TR : Problem with loadBfact.py on windows - FIXED
De : ABEL Stephane 175950 Envoyé : vendredi 10 juillet 2015 18:39 À : pymol-users@lists.sourceforge.net Objet : Problem with loadBfact.py on windows (ABEL Stephane 175950 I have re installed the program and removed an old version of Pymol and now my script works Thanks -- Message: 2 Date: Fri, 10 Jul 2015 12:44:40 + From: ABEL Stephane 175950 stephane.a...@cea.fr Subject: [PyMOL] Problem with loadBfact.py on windows To: pymol-users@lists.sourceforge.net pymol-users@lists.sourceforge.net Message-ID: 3e39b768bb199548ab18f7289e7534af1b471...@exdag0-b0.intra.cea.fr Content-Type: text/plain; charset=iso-8859-1 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,\ -0.30319, -0.10751, -106.549461365,\ 30.012023926, 31.324144363, 31.591945648,\ 66.820175171, 146.280471802, -20.0 ) ###End Script But on windows, i obtained the following errors PyMOLrun ./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' PyMOLloadBfacts 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 -- 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
