Jmol - Revision history

Smith at 22:37, 22 January 2014

2014-01-22T22:37:51Z

2014-01-22T22:36:38Z

‎Loading a PDB file for viewing in JMOL

2013-07-16T19:23:43Z

‎Overview

2011-06-07T21:58:50Z

‎Overview

2011-06-07T21:58:31Z

‎Overview

2011-06-07T21:58:03Z

‎Loading a PDB file

2011-06-07T21:48:39Z

‎Outline

2011-06-07T21:48:29Z

‎Loading a PDB file

2011-06-07T21:47:46Z

‎Jmol Display Options

2011-03-22T16:58:15Z

‎Jmol Display Options

@@ Line 19: / Line 19: @@
 ===To load from a local file===
-# Right-click on the project.
+# Right-click on the [[Workspace]] icon.
 # Select "Open File(s)"
 # Select the file type as "PDB File Format".
@@ Line 27: / Line 27: @@
 ===Open PDB File from RCSB Protein Data Bank===
-# Right-click on the project.
+# Right-click on the [[Workspace]] icon.
 # Select "Open PDB File from RCSB Protein Data Bank.
 # Enter the code for the desired structure, e.g. "1muh".

@@ Line 15: / Line 15: @@
 ==Loading a PDB file for viewing in JMOL==
 # Load the JMOL component in the [[Component_Configuration_Manager|Component Configuration Manager]], if not already done.
 A PDB file can be loaded from disk, or directly from the RCSB Protein Data Bank

← Older revision		Revision as of 19:23, 16 July 2013
Line 9:		Line 9:


−	[[Image:JMOL_Viewer_1MUH.png]]	+	[[Image:JMOL_Viewer_1MUH.png\|{{ImageMaxWidth}}]]

	The file 1muh.pdb displayed in Jmol.		The file 1muh.pdb displayed in Jmol.

← Older revision		Revision as of 21:58, 7 June 2011
Line 9:		Line 9:


−	[[Image:~~JMOL_Viewer~~.png]]	+	[[Image:JMOL_Viewer_1MUH.png]]

	The file 1muh.pdb displayed in Jmol.		The file 1muh.pdb displayed in Jmol.

← Older revision		Revision as of 21:58, 7 June 2011
Line 9:		Line 9:


−	[[Image:~~T_JMOL_Viewer~~.png]]	+	[[Image:JMOL_Viewer.png]]

	The file 1muh.pdb displayed in Jmol.		The file 1muh.pdb displayed in Jmol.

@@ Line 13: / Line 13: @@
 The file 1muh.pdb displayed in Jmol.
-==Loading a PDB file==
+==Loading a PDB file for viewing in JMOL==
-# Create a new project or select an existing project in the Project Folders component.
+A PDB file can be loaded from disk, or directly from the RCSB Protein Data Bank
-# Right-click on the project to bring up the Open File dialog.
 # Select the file type as "PDB File Format".
-# Navigate using the file browswer to the desired PDB format file and read it in.  (these files end with a ".pdb" filename suffix).
+# Locate the desired PDB-format file using the file browser (the browser will display files with a ".pdb" filename suffix).
-# The molecular structure will be displayed in the Jmol component.
+# The molecular structure will be displayed in Jmol.
 ==Jmol Display Options==

← Older revision		Revision as of 21:48, 7 June 2011
Line 3:		Line 3:

	__TOC__		__TOC__
−
−
−	~~==Outline==~~
−
−	~~This tutorial contains~~
−	~~#. an overview of Jmol and~~
−	~~#. instructions on how to view molecular structure (PDB format) files within geWorkbench.~~

@@ Line 31: / Line 31: @@
 ==Jmol Display Options==
-Jmol has a number of optional settings to modify the display.  These include operations to select, render, color and label the molecule and its constituent parts.  As an example, the rendering sub-menu is depicted below:
+All JMOL visualization options are available by right-clicking in the component.   Here we show the menu-item for the solvent accessible surface being chosen.
 ==Increasing memory for very large structures==
 It may occur for very large PDB structures that geWorkbench does not have enough memory available.  This can be remedied by increasing the amount of memory allocated to Java and restarting geWorkbench.  Instructions for increasing the amount of Java memory are available in the [[FAQ|geWorkbench FAQ]].

← Older revision		Revision as of 16:58, 22 March 2011
Line 36:		Line 36:

	Jmol Rendering submenu.		Jmol Rendering submenu.
		+
		+
		+	==Increasing memory for very large structures==
		+
		+	It may occur for very large PDB structures that geWorkbench does not have enough memory available. This can be remedied by increasing the amount of memory allocated to Java and restarting geWorkbench. Instructions for increasing the amount of Java memory are available in the [[FAQ\|geWorkbench FAQ]].