Cheshift - Revision history

Cchem: 1 revision

2017-02-06T03:04:50Z

1 revision

OsvaldoMartin: /* References */

2017-01-16T17:03:23Z

References

Bell: 3 revisions

2014-09-16T03:21:53Z

3 revisions

OsvaldoMartin: /* Version */

2014-09-02T18:18:43Z

Version

OsvaldoMartin: update link to new version

2014-09-02T18:18:27Z

update link to new version

OsvaldoMartin at 21:31, 27 May 2014

2014-05-27T21:31:17Z

Bell: 8 revisions

2014-05-26T23:33:24Z

8 revisions

OsvaldoMartin at 19:46, 25 May 2014

2014-05-25T19:46:59Z

OsvaldoMartin: /* References */

2014-05-23T20:44:57Z

References

OsvaldoMartin: /* License */

2014-05-23T20:43:58Z

License

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 * 2012-02-14 (Version 2.0)
 This version was able to establish a connection to the version of the <i>Che</i>Shift Server described in [2]
 == References ==
 [1] Martin O.A. Arnautova Y.A. Icazatti A.A. Scheraga H.A. and Vila J.A. A Physics-Based Method to Validate and Repair Flaws in Protein Structures. Proc Natl Acad Sci USA 2013, vol. 110 16826-16831.
-[2] Martin O.A. Vila J.A. and Scheraga H.A. (2012). <i>Che</i>Shift-2: Graphic validation of protein structures. Bioinformatics 2012. 28(11), 1538-1539.
+[2] Vila J.A. Arnautova Y.A. Martin O.A. and Scheraga, H.A. (2009). Quantum-mechanics-derived <sup>13</sup>C chemical shift server (<i>Che</i>Shift) for protein structure validation. PNAS, 106(40), 16972-16977.
-[4] Vila, J.A. and Scheraga H.A. (2009). Assessing the accuracy of protein structures by quantum mechanical computations of <sup>13</sup>C<sup>α</sup> chemical shifts. Accounts of chemical research, 42(10), 1545-53.
+[3] Vila, J.A. and Scheraga H.A. (2009). Assessing the accuracy of protein structures by quantum mechanical computations of <sup>13</sup>C<sup>α</sup> chemical shifts. Accounts of chemical research, 42(10), 1545-53.
 [[Category:Plugins]]
 [[Category:Pymol-script-repo]]

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 === Version ===
-The current version of this plugin is 3.5
+The current version of this plugin is 3.6
 == Installation ==

@@ Line 1: / Line 1: @@
 {{Infobox script-repo
 |type      = plugin
-|download  = https://github.com/aloctavodia/cheshift/archive/v3.5.zip
+|download  = https://github.com/aloctavodia/cheshift/archive/v3.6.zip
 |author    = [[User:OsvaldoMartin|Osvaldo Martin]]
 |license   = GPL
@@ Line 22: / Line 22: @@
 == Installation ==
 === Linux ===
-) The plugin can be downloaded from here [[https://github.com/aloctavodia/cheshift/archive/v3.1.zip Here]]
+) The plugin can be downloaded from here [[https://github.com/aloctavodia/cheshift/archive/v3.6.zip Here]]
 ) If you are using the incentive version of PyMOL skip the next step and go directly to step 4.
@@ Line 34: / Line 34: @@
 This plugin have not been extensively tested on Windows machines, but it passed all the test I have done...
-) The plugin can be downloaded from here [[https://github.com/aloctavodia/cheshift/archive/v3.1.zip Here]]
+) The plugin can be downloaded from here [[https://github.com/aloctavodia/cheshift/archive/v3.6.zip Here]]
 ) If you are using the incentive version of PyMOL skip the next step and go directly to step 4.
@@ Line 46: / Line 46: @@
 This plugin have not been extensively tested on Windows machines, but it passed all the test I have done...
-) The plugin can be downloaded from here [[https://github.com/aloctavodia/cheshift/archive/v3.1.zip Here]]
+) The plugin can be downloaded from here [[https://github.com/aloctavodia/cheshift/archive/v3.6.zip Here]]
 ) If you are using the incentive version of PyMOL skip the next step and go directly to step 4.
@@ Line 89: / Line 89: @@
 == Change log ==
 * 2014-05-23 (Version 3.5)

@@ Line 40: / Line 40: @@
 ) You should install NumPy and SciPy. Probably the easiest way to do this on a Windows machine is to install a Python Distribution like [[https://store.continuum.io/cshop/anaconda/ Anaconda]] or [[https://www.enthought.com/products/canopy/  Canopy]]
-) Open PyMOL and then go to plugin --> plugin manager --> Install New Plugin --> Install from local file --> Choose file. and choose the zip file you download in step 1. Now the plugin should be installed.
+) Open PyMOL and then go to plugin --> plugin manager --> Install New Plugin --> Install from local file --> Choose file. and choose the zip file you download in step 1. On Windows machine this step could take a couple of minutes, just wait for the confirmation message. Now the plugin should be installed.
 If you have an old version of PyMOL without the plugin manager then, unzip the file downloaded in step 1 and copy the "cheshift" folder to the plugin directory, probably something like "C:\Python27\Lib\site-packages\pmg_tk\startup\"

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 Blue is used to highlight residues for which the agreement between observed and predicted <sup>13</sup>C<sup>α</sup> and <sup>13</sup>C<sup>β</sup>chemical shifts can be improved, i.e., if the (χ<sup>1</sup> /χ<sup>2</sup> ) side-chain  | 440px]]
-The differences between observed and predicted <sup>13</sup>C<sup>α</sup> and <sup>13</sup>C<sup>β</sup> chemical shifts can be used as a sensitive probe with which to detect possible local flaws in protein structures. For this reason exist [http://www.cheshift.com CheShift], a Web server for protein structure validation.
+CheShift (pronounced /tʃeʃɪft/) is a software for prediction of 13Cα and 13Cβ chemical shifts and validation of proteins structures. It is based on the idea that the differences between observed and predicted <sup>13</sup>C<sup>α</sup> and <sup>13</sup>C<sup>β</sup> chemical shifts can be used as a sensitive probe with which to detect possible local flaws in protein structures. A [http://www.cheshift.com Web Server] is also available.
 This plugin provides a way to use PyMOL to validate a protein model using observed chemical shifts.

← Older revision	Revision as of 03:04, 6 February 2017
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← Older revision	Revision as of 03:21, 16 September 2014
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← Older revision	Revision as of 23:33, 26 May 2014
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 [2] Martin O.A. Vila J.A. and Scheraga H.A. (2012). <i>Che</i>Shift-2: Graphic validation of protein structures. Bioinformatics 2012. 28(11), 1538-1539.
-[3] Vila J.A. Arnautova Y.A. Martin O.A. and Scheraga, H.A. (2009). Quantum-mechanics-derived 13C chemical shift server (<i>Che</i>Shift) for protein structure validation. PNAS, 106(40), 16972-16977.
+[3] Vila J.A. Arnautova Y.A. Martin O.A. and Scheraga, H.A. (2009). Quantum-mechanics-derived <sup>13</sup>C chemical shift server (<i>Che</i>Shift) for protein structure validation. PNAS, 106(40), 16972-16977.
 [4] Vila, J.A. and Scheraga H.A. (2009). Assessing the accuracy of protein structures by quantum mechanical computations of <sup>13</sup>C<sup>α</sup> chemical shifts. Accounts of chemical research, 42(10), 1545-53.

@@ Line 84: / Line 84: @@
 == License ==
-<i>Che</i>Shift plugin is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License. A complete copy of the GNU General Public License can be accessed here http://www.gnu.org/licenses/.
+<i>Che</i>Shift plugin is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License. A complete copy of the GNU General Public License can be accessed [http://www.gnu.org/licenses here].
-<i>Che</i>Shift uses data derived from the [[http://dunbrack.fccc.edu/ndrd/ Neighbor-Dependent Ramachandran Distributions]] obtained by the Dunbrack Lab. This derived data is also released under the GPL license, with the permission of Professor Roland Dunbrack. The full NDRD data is released using a different [[http://dunbrack.fccc.edu/ndrd/license/index.html license]].
+<i>Che</i>Shift uses data derived from the [http://dunbrack.fccc.edu/ndrd/ Neighbor-Dependent Ramachandran Distributions] obtained by the Dunbrack Lab. This derived data is also released under the GPL license, with the permission of Professor Roland Dunbrack. The full NDRD data is released using a different [http://dunbrack.fccc.edu/ndrd/license/index.html license].
 == Change log ==