Jmol as editor - Revision history

EricMartz at 21:15, 3 January 2021

2021-01-03T21:15:26Z

Rhuehne: /* Moving atoms */

2015-04-27T09:47:09Z

‎Moving atoms

Rhuehne: /* Moving atoms */

2015-04-27T09:45:49Z

‎Moving atoms

AngelHerraez: Adding hydrogens

2010-02-12T20:16:15Z

Adding hydrogens

AngelHerraez: brief details and links

2008-11-15T17:33:57Z

brief details and links

AngelHerraez: first draft

2008-11-11T19:49:50Z

first draft

New page

Although Jmol is by design a viewer for molecular structures, its growth has brought some limited capabilities for editing the model.
By editing, we mean altering atom positions or identities (e.g. chemical element), addition or removal of some atoms.

== Modifying bonds ==

set autoBond

connect

calculate hBonds

calculate aromatic

calculate structure -- not really bonds

== Moving atoms ==

translateSelected

rotateSelected

invertSelected

minimize

== Adding atoms ==

data

== Removing atoms ==

zap frame

← Older revision		Revision as of 21:15, 3 January 2021
Line 45:		Line 45:
	[http://chemapps.stolaf.edu/jmol/docs/#zap zap]		[http://chemapps.stolaf.edu/jmol/docs/#zap zap]
	allows to delete all atoms in a certain model/frame.		allows to delete all atoms in a certain model/frame.
		+
		+	== PDB file editing with Jmol ==
		+	* [http://proteopedia.org/wiki/index.php/Jmol/PDB_file_editing_with_Jmol PDB file editing with Jmol]. How to put the loaded PDB file into an array of lines, edit those lines with Jmol commands, and write a new PDB file. Also how to put Jmol commands in REMARK lines in the headers of PDB or PNGJ files.

@@ Line 32: / Line 32: @@
 changes atom coordinates following a force field calculation in search of a conformation of minimal energy.
-See also section [http://wiki.jmol.org/index.php/Mouse_Manual#How_to_change_atom_coordinates How_to_change_atom_coordinates] in the [http://wiki.jmol.org/index.php/Mouse_Manual mouse manual].
+See also section [http://wiki.jmol.org/index.php/Mouse_Manual#How_to_change_atom_coordinates How to change atom coordinates] in the [http://wiki.jmol.org/index.php/Mouse_Manual mouse manual].
 == Adding atoms ==

@@ Line 31: / Line 31: @@
 [http://chemapps.stolaf.edu/jmol/docs/#minimize minimize]
 changes atom coordinates following a force field calculation in search of a conformation of minimal energy.
 == Adding atoms ==

@@ Line 36: / Line 36: @@
 [http://chemapps.stolaf.edu/jmol/docs/#data data]
 allows to add atoms and to add or redefine atom-associated properties (such as coordinates, charge, radius, temperature factor, occupancy, vibration, etc., or custom properties).
 == Removing atoms ==

@@ Line 4: / Line 4: @@
 == Modifying bonds ==
-set autoBond
+[http://chemapps.stolaf.edu/jmol/docs/#set_autobond set autoBond]
-connect
+[http://chemapps.stolaf.edu/jmol/docs/#connect connect]
-calculate hBonds
+[http://chemapps.stolaf.edu/jmol/docs/#calculate calculate hBonds]
-calculate aromatic
+[http://chemapps.stolaf.edu/jmol/docs/#calculate calculate aromatic]
-calculate structure -- not really bonds
+[http://chemapps.stolaf.edu/jmol/docs/#calculate calculate structure] does not really change bonds, but assignation of secondary structure for proteins and, hence, cartoon/ribbon rendering and coloring by structure.
 == Moving atoms ==
-translateSelected
+[http://chemapps.stolaf.edu/jmol/docs/#translateSelected translateSelected]
-rotateSelected
+[http://chemapps.stolaf.edu/jmol/docs/#rotateSelected rotateSelected]
-invertSelected
+[http://chemapps.stolaf.edu/jmol/docs/#invertSelected invertSelected]
-minimize
+[http://chemapps.stolaf.edu/jmol/docs/#minimize minimize]
 == Adding atoms ==
-data
+[http://chemapps.stolaf.edu/jmol/docs/#data data]
 == Removing atoms ==
-zap frame
+[http://chemapps.stolaf.edu/jmol/docs/#zap zap]