CMPyMOL - Revision history

Cchem: 1 revision

2016-05-31T05:42:48Z

1 revision

Speleo3: fix download url

2016-05-05T15:06:28Z

fix download url

Pyadmin: 26 revisions

2014-03-28T01:06:30Z

26 revisions

Venky at 19:55, 21 May 2013

2013-05-21T19:55:06Z

Venky: /* Screenshot */

2013-05-21T19:53:53Z

Screenshot

Venky at 21:23, 20 May 2013

2013-05-20T21:23:41Z

Venky: /* Plots */

2013-05-20T20:54:12Z

Plots

Venky: /* Requests and Disclaimer */

2013-05-20T20:44:26Z

Requests and Disclaimer

Venky: /* Requests and Disclaimer */

2013-05-20T20:44:03Z

Requests and Disclaimer

Venky: /* Software */

2013-05-20T20:42:20Z

Software

@@ Line 1: / Line 1: @@
 {{Infobox script-repo
 |type      = Software
-|download = http://emptyewer.github.io/CMPyMOL/
+|download  = https://github.com/emptyewer/CMPyMOL
 |version = 1.0b
 |author    = [[User:Venky|Venkatramanan Krishnamani]]

← Older revision		Revision as of 19:55, 21 May 2013
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	[[File:CMPyMOL.PNG\|thumb\|877px\|center]]		[[File:CMPyMOL.PNG\|thumb\|877px\|center]]
		+
		+	== Pairwise Aminoacid Heatmap ==
		+	[[File:Heatmap-CMPyMOL.PNG\|thumb\|877px\|center]]

	== License ==		== License ==

@@ Line 97: / Line 97: @@
 Users are welcome to send me an email to request the addition of a specific feature or to report a bug.
-== Screenshot ==
+== Main Window ==
 [[File:CMPyMOL.PNG|thumb|877px|center]]

@@ Line 7: / Line 7: @@
 }}
-CMPyMOL is an add-on software to molecular visualization program PyMOL. It combines the 3D visualization capabilities of PyMOL and 2D protein contact maps with an interactive interface for scientific analysis. This software is freely distributed under the MIT license for Linux and Mac OS X platforms.
+CMPyMOL is an add-on software to molecular visualization program PyMOL. It combines the protein 3D visualization capabilities of PyMOL and the protein's 2D contact map with an interactive interface for scientific analysis. This software is freely distributed under the MIT license for Linux and Mac OS X platforms.
 == Website ==
 http://emptyewer.github.io/CMPyMOL/
 == Prerequisites ==
@@ Line 21: / Line 29: @@
 ** [http://www.pythonware.com/products/pil/ python imaging library (PIL)]
 ** [http://www.numpy.org numpy]
-* PyMOL executable. It is recommended that the user make sure the directory of installed executable is listed in the $PATH variable.
+* PyMOL. (It is recommended that the user add the PyMOL installation directory to the $PATH environment variable.)
-* Stride executable. This can be downloaded from http://webclu.bio.wzw.tum.de/stride/ and easily compiled into an executable. It is recommemded that the executable or its directory is listed in the system variable $PATH. NOTE: If this executable is not installed properly, the secondary structure calculation will be automatically disabled.
+* Stride secondary structure assignment tool. This program can be downloaded from http://webclu.bio.wzw.tum.de/stride/ and compiled into a stand-alone executable. It is recommended that the Stride executable or its installation directory is added to the $PATH environment variable. NOTE: If this executable is not detected in the $PATH variable, the secondary structure calculation will be disabled in CMPyMOL.
 === Mac OS X ===
-* Users can install the python libraries using "easy_install" or "pip". It is recommened that the user downloads Enthough Canopy python distribution and management package from https://www.enthought.com/products/canopy/. This package includes a robust python library management software and a python IDE.
+* Users can install the python libraries using "easy_install" or "pip". It is recommended that the user use Enthought Canopy python distribution and management package downloaded from https://www.enthought.com/products/canopy/. This package includes a robust python library management software and a python IDE.
-* PyMOL 1.5.x can be installed using MacPorts http://www.macports.org. NOTE: This automatically adds the executable into $PATH.
+* PyMOL 1.5.x can be installed using MacPorts http://www.macports.org. NOTE: This automatically adds the executable into the $PATH environment variable.
 === Linux ===
-* The python dependencies and PyMOL can be installed using apt-get (aptitude) or similar package management system.
+* The python dependencies and PyMOL can be installed using apt-get (aptitude) or a similar package management system.
 == Installation ==
-There is no need for installation of the script. Optionally, a standalone executable can be complied using "pyinstaller" or "py2exe" or "py2app" packages depending on the users operating system.
+There is no need for installation of the script. Optionally, a standalone executable can be complied using "pyinstaller" or "py2exe" or "py2app" package, depending on the users operating system.
 == Usage ==
 <source lang="bash">
-python CMPyMOL.py
+python /<path to CMPyMOL directory>/CMPyMOL.py
 </source>
@@ Line 46: / Line 54: @@
 == Software ==
-Clicking (left) and draging a selection of points on the displayed contact map will highlight the corresponding residues involved in that contact in the PyMOL window (as red and blue colored spheres). In addition, several structural/biochemical properties can be overlayed on top of the contact map (listed below). The contact-map data can also be plotted in other representations. The calculated contact-map, heat-map and contact density information is now stored in a local SQL database. Any subsequent access of the same PDB with matching parameters will be read from the database for fast access. The code for calculating contact map for trajectory files is parallelized for efficiency.
+Clicking (left) and dragging a selection of contact points on the displayed contact map will highlight the corresponding residues in the PyMOL window (as red and blue colored atoms in spheres representation). In addition, several structural/biochemical properties can be overlaid on top of the contact map. The contact-map data can also be plotted in other representations. The calculated contact-map, heat-map and contact density information is stored in a local SQL database. Any subsequent access of the same PDB with matching parameters will be read from the database for fast access. The code for calculating contact map for trajectory files is parallelized for efficiency.
 === Inputs ===
 * Single-frame PDB files (local)
 * Multi-frame PDB trajectory files (local)
-* Multi-frame trajectory files should have the following format. The PDB can include REMARKS, CRYST and other standard information lines about the PDB, but MODEL line is essential for the software to work properly (ENDMDL is optional).
+* Multi-frame trajectory files should have the following format.
 <source lang="bash">
@@ Line 65: / Line 73: @@
 ENDMDL
 </source>
 === Overlays ===
-* Secondary structure of the protein as translucent strips over the contact map. This button won't be active if secondary structure calculation program stride is not installed. (Button: Secondary Structure)
+* Secondary structure of the protein is overlaid as translucent strips over the contact map. This button won't be active if secondary structure calculation program stride is not found in the system path ($PATH). (Button: Secondary Structure)
-* Contact points where a Charge-Charge interaction occurs. (Button: Charged Interactions)
+* Contact points where a Charge-Charge interaction occurs are highlighted. (Button: Charged Interactions)
-* Residues that interact via hydrophobic interaction. (Button: Hydrophobic Interactions)
+* Residues that interact via hydrophobic interaction are highlighted. (Button: Hydrophobic Interactions)
-* Contact regions that have a b-factor that is higher than a certain cutoff (Button: B-factor). The b-factor cutoff can be varied using a slider (Slider).
+* Contact regions that have a B-factor that is higher than a certain cutoff are highlighted (Button: B-factor). The b-factor cutoff can be varied using a slider (Slider).
-* Highlights a contact point/region where the selected pair of residues are in contact (selected by checking the checkbox). If only one aminoacid is selected from the list, interaction site of the selected aminoacid with another one of the same type is highlighted. (List of checkboxes for each aminoacid)
+* Highlights a contact point/region where the pair of selected residues are in contact (selected by checking the checkboxes). If only one aminoacid is selected from the list, interaction site of the selected aminoacid with another one of the same type is highlighted. (List of checkboxes for each aminoacid)
 ===  Plots ===
-* Pairwise Heat Map - Plots a 20x20 matrix of count of pairwise aminoacid interactions.
+* Pairwise Heat Map - Plots a 20x20 matrix of pairwise aminoacid interaction count.
-* Contacts Histogram - Plots the number of contacts formed by a given residue as a bar graph. Selecting a particular bar highlights the corresponding residue in the PyMOL window.
+* Contacts Histogram - Plots the number of contacts around a given residue. Selecting a particular bar highlights the corresponding residue in the PyMOL window.
-* Variance Contact Map - For Multi-frame PDB files (trajectory), this button toggles the display of the variance contact map calculated starting from the initial frame until the current frame. This view can be used to identifying the dynamic regions of a protein.
+* Variance Contact Map - For Multi-frame PDB files (trajectory), this button toggles the displays the variance contact map starting from the initial frame until the current frame. This view can be used to identifying the dynamic regions in a protein.
 == Requests and Disclaimer ==

@@ Line 76: / Line 76: @@
 * Pairwise Heat Map - Plots a 20x20 matrix of count of pairwise aminoacid interactions.
 * Contacts Histogram - Plots the number of contacts formed by a given residue as a bar graph. Selecting a particular bar highlights the corresponding residue in the PyMOL window.
-* Variance Contact Map - For Multi-frame PDB files (trajectory), this button toggles the displays the variance of the contact map starting from the initial frame until the current frame. This is extremely useful in identifying the dynamic regions of a protein.
+* Variance Contact Map - For Multi-frame PDB files (trajectory), this button toggles the display of the variance contact map calculated starting from the initial frame until the current frame. This view can be used to identifying the dynamic regions of a protein.
 == Requests and Disclaimer ==

← Older revision	Revision as of 05:42, 31 May 2016
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← Older revision	Revision as of 01:06, 28 March 2014
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 == Requests and Disclaimer ==
-Users are welcome to send me an email to request the addition of a specific feature. I am actively developing this software.
+Users are welcome to send me an email to request the addition of a specific feature or report a bug in the software.
 == Screenshot ==