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Marcel Patek
117 followers -
Passionate chemist with interest in life sciences, technology, photography, and drug discovery.
Passionate chemist with interest in life sciences, technology, photography, and drug discovery.

117 followers
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Marcel Patek's posts

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Preparing 3-D molecular structures

A short tutorial demonstrating the use of free molecular drawing application MarvinSketch from ChemAxon. The main purpose is to prepare a molecular structure file which will serve as an input to a variety of computational packages and downstream evaluation of molecular properties. 

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NBO Scripts and Handy Applications website revamped.

After several months of mostly weekend work, the site has new look and structure. It was structured by the tool and programing language used to process .nbo files. Now, it also includes sections with tutorials and member area.

... #NBO website strives to bring useful tools of Natural Bond Orbital analysis into one place while encouraging readers, researchers, and teachers to share their experience and ideas to further facilitate analysis, interpretation, and visualization of NBOs...

Enjoy. http://nbo.marcelpatek.com 

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Natural Dipole Analysis with IPython Notebook:

Understanding electrostatic interactions in molecules and molecular complexes provides the basis for interpretation of chemical reactions and molecular interactions. First of the series of "Analyzing NBO output with IPython notebook" is the example of decomposing NLMO dipole vectors into a vector path that can be displayed as images and further analyzed for intramolecular dipole components.
Full blog is at http://bit.ly/1UflF5Z and includes link to the IPython (Jupyter) notebook.
#NBO   #Jupyter  
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Dynamic Web Visualization of NBOs Based on jvxl Surface Files.

Here comes the second post on the visualization of #NBO s in a static website. Steps for getting the key elements for building the website are described. The visualization is based on jvxl surface files and support of #JSmol . With the help of css, JavaScript, and JQuery, a simple interaction with molecular and surface models has been demonstrated. All files used in the post are available from the Download section.

The full description is in the Blog is at: http://bit.ly/1VTPhEi

The demo webpage can be viewed at:
                   http://nbo.marcelpatek.com/mol/demo/jsmolweb
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2015-08-01
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Web Visualization of NBOs in x3d Format.

Another post from the #NBO  series explores the generation and implementation of .x3d 3-D files for visualization of Natural Bond Orbitals in web browsers. Jmol-NBO Visualization Helper was used to create the Jmol .macro files and scripts that immediately assist in writing the corresponding .x3d files off the #Jmol  application. Finally, a simple web page container is built to allow web-presentation and discussion of NBO imagery.

See the demo site at:   http://nbo.marcelpatek.com/mol/demo/x3d
As usual, the full blog is at:  http://bit.ly/1JohA8R
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2015-07-26
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Update on Visualization of Natural Bond Orbitals (NBO) in a web browser.

Now with JSmol in the Jmol Web Page Maker.  
http://bit.ly/T8A3v7

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Analyzing NBO Results with IPython Notebook

#Python  has become an increasingly important programming language for data processing and analysis. This blog introduces the use of #IPythonNotebook : a web-based interactive computing environment for exploratory and reproducible processing of results. With the #IPython  Notebook, one creates documents, called notebooks that contain formatted text, figures, equations, programming code, and code output that can be shared with others to enhance teaching effectiveness. Presented examples of IPython Notebook comprise processing, analysis, and visualization of computational chemistry results.

More specifically, processing an output from the Natural Bond Orbital (NBO) analysis of molecular properties is discussed. The first example includes extracting DIPOLE MOMENT ANALYSIS summary from the typical NBO/GENNBO output file and creating an html formatted table in the IPython Notebook.

See the blog at:  http://bit.ly/1BuFZmb
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Natural Bond Orbitals (NBO) in Organic Chemistry
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Knime, Python nodes, and Anaconda virtual environment

With the release 2.11 of the #KNIME  Analytics Platform, integration of #Python  programming language was brought to a new level. The most important change has been a move toward the original CPython implementation. There is an introductory webinar available at YouTube ( http://youtu.be/9RkRHI32Dy8 ) that outlines new features and provides a brief demo of Python nodes. After working for a few days with the new KNIME Desktop, I summarized some tips on how to use working Python virtual environment and run the Python nodes in KNIME.
Besides setting up the virtual environment in #Anaconda , a step-by-step guide for installing required protobuf library under Windows 7 was added together with a loose summary of input & output syntax in the new Python Script nodes.

http://script-orgmedchem.blogspot.com/2014/12/knime-python-nodes-and-anaconda-virtual.html
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Knime-Python-Anaconda and Pandas

To facilitate analysis and visualization of natural dipole moments obtained from the Natural Bond Orbital ( #NBO ) analysis of molecular wavefunction,   #KNIME   workflow implementing #Python   script nodes is described. Python libraries such as Numpy and Pandas are used to demonstrate benefits of Python implementation. Complete workflow with exemplary files is available for download at:

http://script-orgmedchem.blogspot.com/2014/12/knime-python-anaconda-and-pandas.html
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2014-12-19
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Jmol-NBO Visualization Helper ver 2.0:

#JmolNbo  Visualization Helper generates sets of #Jmol  macro files as inputs into Jmol molecular visualizer. Specific #NBO orbitals and NBO-NBO* pairs can be easily visualized and their interaction analyzed. Additional features include options to write macro files into default Jmol directory and to inspect generated .nbo files for key interacting orbitals. The latest improvements added options for visualization of 2-D contour images in customizable planes and option to generate imagery for spin-polarized unrestricted solutions (alpha and beta spin orbitals).
#Java  app GUI is now running both under Windows and Linux (Ubuntu) systems.

See more at: http://bit.ly/11ybrAK
Download at: http://www.marcelpatek.com/nbo/nbo.html
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