Pudge - Revision history

Smith: /* Parameters and running Pudge */

2015-02-11T15:54:26Z

‎Parameters and running Pudge

2015-02-11T15:50:15Z

‎Parameters and running Pudge

2015-02-11T15:48:40Z

‎Parameters and running Pudge

2015-01-28T00:32:24Z

‎Parameters and running Pudge

2014-11-25T20:32:41Z

‎Parameters and running Pudge

2014-11-25T20:31:54Z

‎Parameters and running Pudge

2014-11-25T20:25:16Z

‎External Tutorial

2014-01-23T00:25:52Z

2013-07-16T19:42:50Z

‎Parameters and running Pudge

2012-07-20T19:21:01Z

‎References

← Older revision		Revision as of 15:54, 11 February 2015
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−	3. '''Click Analyze''' - ~~The~~ Pudge Analysis ~~inteface~~ will be displayed either directly in geWorkbench, using a built-in browser, or in the case where a 64-bit Java Virtual Machine is in use (now the default on all platforms) the user can click a link to display the analysis page in an external web browser window.	+	3. '''Click Analyze''' - In the PudgeBrowser tab, the Pudge Analysis interface will be displayed either directly in geWorkbench, using a built-in browser, or in the case where a 64-bit Java Virtual Machine is in use (now the default on all platforms) the user can click a link to display the analysis page in an external web browser window.

	The Pudge analysis web page contains a number of configuration options.		The Pudge analysis web page contains a number of configuration options.

@@ Line 35: / Line 35: @@
-. click Analyze.
+. '''Click Analyze''' - The Pudge Analysis inteface will be displayed either directly in geWorkbench, using a built-in browser, or in the case where a 64-bit Java Virtual Machine is in use (now the default on all platforms) the user can click a link to display the analysis page in an external web browser window.
 The Pudge analysis web page contains a number of configuration options.
@@ Line 48: / Line 46: @@
-. Select any desired methods.  More than one per step can be chosen by use of the control key (Windows) while clicking in the menu.  Once all selections have been made, click on Go to launch the job.
+. '''Select any desired methods''' - More than one per step can be chosen by use of the control key (Windows) while clicking in the menu.  Once all selections have been made, click on Go to launch the job.
 Results will be displayed in a web browser window, either your external browser or within geWorkbench (mostly no longer supported).  From there, once can save result files in PDB format and load them into geWorkbench for viewing and further manipulation.

← Older revision		Revision as of 15:48, 11 February 2015
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−	3. click Analyze. ~~In most cases~~, ~~this will cause~~ the ~~PudgeBrowser tab~~ to ~~just~~ display ~~a link that will open~~ in an external ~~browswer~~. ~~That~~ page~~, whether displayed in geWorkbench or in the external browser,~~ contains a ~~large~~ number of ~~additional~~ configuration options.	+	3. click Analyze.
		+
		+	The Pudge Analysis inteface will be displayed either directly in geWorkbench, using a built-in browser, or in the case where a 64-bit Java Virtual Machine is in use (now the default on all platforms) the user can click a link to display the analysis page in an external web browser window.
		+
		+	The Pudge analysis web page contains a number of configuration options.

	Explanations of each available method can be obtained by clicking on its entry in the interface.		Explanations of each available method can be obtained by clicking on its entry in the interface.

@@ Line 22: / Line 22: @@
 To run Pudge,
-. add a job name in the Job Name text field.
+. '''Job Name''' - add a job name in the Job Name text field.
-. optionally, add a PDB protein structure file to serve as a starting structural template.
+. '''Browse for Native Structure (optional)''' - this is not currently working.  The intended use was to add a PDB protein structure file to serve as a starting structural template.

@@ Line 46: / Line 46: @@
 . Select any desired methods.  More than one per step can be chosen by use of the control key (Windows) while clicking in the menu.  Once all selections have been made, click on Go to launch the job.
-Results will be displayed in a web browser window within geWorkbench.  From there, once can save result files in PDB format and load them into geWorkbench for viewing and further manipulation.
+Results will be displayed in a web browser window, either your external browser or within geWorkbench (mostly no longer supported).  From there, once can save result files in PDB format and load them into geWorkbench for viewing and further manipulation.
 ==References==

← Older revision		Revision as of 20:31, 25 November 2014
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−	3. click Analyze. ~~This~~ will cause a ~~web browser~~ page ~~to be~~ displayed ~~which~~ contains a large number of additional configuration options.	+	3. click Analyze. In most cases, this will cause the PudgeBrowser tab to just display a link that will open in an external browswer. That page, whether displayed in geWorkbench or in the external browser, contains a large number of additional configuration options.

	Explanations of each available method can be obtained by clicking on its entry in the interface.		Explanations of each available method can be obtained by clicking on its entry in the interface.

@@ Line 9: / Line 9: @@
 ==External Tutorial==
-The Honig lab has provided their own [http://luna.bioc.columbia.edu/honiglab/pudge/documentation/tutorial.html tutorial for Pudge].
+The Honig lab has provided their own [http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PUDGE_Tutorial tutorial for Pudge].
 In addition, Pudge can be run [http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:PUDGE directly on their web server].

← Older revision		Revision as of 00:25, 23 January 2014
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	==Parameters and running Pudge==		==Parameters and running Pudge==

−	If Pudge has been loaded via the CCM, it will appear in the Analysis area when a FASTA sequence file is loaded and selected in the ~~Project Folders area~~.	+	If Pudge has been loaded via the CCM, it will appear in the Analysis area when a FASTA sequence file is loaded and selected in the [[Workspace]].

← Older revision		Revision as of 19:42, 16 July 2013
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−	[[Image:Pudge_Parameters.png]]	+	[[Image:Pudge_Parameters.png\|{{ImageMaxWidth}}]]

	To run Pudge,		To run Pudge,

@@ Line 50: / Line 50: @@
 ==References==
 Norel R., Petrey D., and Honig B.: PUDGE: a flexible, interactive server for protein structure prediction. Nucleic Acids Research, 2010, Vol. 38, W550-W554 (Web Server issue). [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896183  link to paper]
 Petrey D. and Honig B.:  Protein structure prediction: inroads to biology. Mol Cell. 2005 Dec 22;20(6):811-9.  [http://www.ncbi.nlm.nih.gov/pubmed/16364908 link to paper]