Coordinate Systems - Revision history

AngelHerraez: documenting screen coordinates

2018-08-25T10:29:44Z

documenting screen coordinates

AngelHerraez: documenting screen coordinates

2018-08-24T08:27:40Z

documenting screen coordinates

AngelHerraez: documenting screen coordinates

2018-08-24T08:21:59Z

documenting screen coordinates

AngelHerraez: documenting screen coordinates

2018-08-23T18:44:37Z

documenting screen coordinates

AngelHerraez: documenting screen coordinates

2018-08-23T10:55:26Z

documenting screen coordinates

New page

== Coordinate systems in Jmol ==

When a file is loaded, the model contains a 3D space system of coordinates and the values of x,y,z for every atom. This coordinate system is inherent to the model. If you load several models, each one brings its own coordinates, so you will usually see both models positioned very far apart, or sometimes overlapping.

Jmol uses this 3D coordinates for all the operations.

Some commands, however, refer to a 2D space, the projection that the observer sees; these are the "screen coordinates".

=== Retrieving 3D coordinates ===
The position of the origin and the orientation of the x,y,z axes may be anyone with respect to the viewer (i.e. the screen display) when a model file is loaded. The command <code>axes on</code> will let you check those.

Examples of how to check the coordinates of an atom:
(<code>p1</code> is a variable used to hold the values and <code>print</code> allows to see its value)
<pre>
p1 = {atomNo=6}.xyz;
print p1.x;
print p1.y;
print p1.z;

p1 = {atomNo=6}.x;
print p1;
p1 = {atomNo=6}.y;
print p1;
p1 = {atomNo=6}.z;
print p1;
</pre>

=== Retrieving screen coordinates ===
Screen coordinates sx,sy,sz are defined as:
* sx from the left border
* sy from the bottom border
* sz from the front (small sz for positions at the front, near the observer; large sz for positions at the rear, far from the observer)
<pre>
p2 = {atomNo=6}.sx;
print p2;
p2 = {atomNo=6}.sy;
print p2;
p2 = {atomNo=6}.sz;
print p2;
</pre>

=== Converting between 3D coordinates and screen coordinates ===

@@ Line 5: / Line 5: @@
 Some commands, however, refer to a 2D space, the projection that the observer sees; these are the "screen coordinates".
-Jmol uses these 3D coordinates for all the operations. Note also that, when the model is rotated or translated (either by mouse action or by commands) the coordinate system and axes move together with the model. That is, position of the model in the 3D coordinate system is always the same; it's just the viewpoint that changes (and, accordingly, the screen coordinates do change with any rotation, translation or zoom).
+Jmol uses the 3D coordinates for nearly all the operations. Note also that, when the model is rotated or translated (either by mouse action or by commands) the coordinate system and axes move together with the model. That is, position of the model in the 3D coordinate system is always the same; it's just the viewpoint that changes (and, accordingly, the screen coordinates do change with any rotation, translation or zoom).
 === Commands that use each coordinate system ===
 ==== 3D coordinates ====
-label
+<code>measure</code>
-measure
+<code>set echo</code> (3D variety)
+:The special syntax for the echo command that provides 3D coordinates of a point to which the echo will be attached (and hence the echo will rotate and translate with the model). [{{ScriptingDoc}}#setecho Command syntax]
-echo (3D variety)
+: Example: <code>set echo id myFirstEcho {1.2 -4.0 1.1}; echo This is the position in 3D;</code>
 ==== Screen coordinates ====
+<code>set echo</code> (2D variety)
-echo
+:The more standard syntax of the echo command positions text with reference to the screen 2D space (hence the text does not move when the model is rotated or translated). [{{ScriptingDoc}}#setecho Command syntax]
+: Examples:
 === Retrieving 3D coordinates ===

← Older revision		Revision as of 08:27, 24 August 2018
Line 6:		Line 6:

	Jmol uses these 3D coordinates for all the operations. Note also that, when the model is rotated or translated (either by mouse action or by commands) the coordinate system and axes move together with the model. That is, position of the model in the 3D coordinate system is always the same; it's just the viewpoint that changes (and, accordingly, the screen coordinates do change with any rotation, translation or zoom).		Jmol uses these 3D coordinates for all the operations. Note also that, when the model is rotated or translated (either by mouse action or by commands) the coordinate system and axes move together with the model. That is, position of the model in the 3D coordinate system is always the same; it's just the viewpoint that changes (and, accordingly, the screen coordinates do change with any rotation, translation or zoom).
		+
		+	=== Commands that use each coordinate system ===
		+	==== 3D coordinates ====
		+
		+	label
		+
		+	measure
		+
		+	echo (3D variety)
		+
		+	==== Screen coordinates ====
		+
		+	echo
		+

	=== Retrieving 3D coordinates ===		=== Retrieving 3D coordinates ===

← Older revision		Revision as of 18:44, 23 August 2018
Line 41:		Line 41:

	=== Converting between 3D coordinates and screen coordinates ===		=== Converting between 3D coordinates and screen coordinates ===
		+	This gives the screen coordinates {sx, sy, sz} corresponding to the 3D coordinates {x, y, z}:
		+	point({x,y,z}, true);
		+	Examples of use:
		+	<pre>
		+	p3 = point( {atomNo=6}, true)
		+	print p3.x; // same as print {atomNo=6}.sx;
		+	print p3.y; // same as print {atomNo=6}.sy;
		+
		+	p3 = point( {4.65, -9.80, 1.21}, true)
		+	print p3.x;
		+	print p3.y;
		+	</pre>
		+
		+	And this does the opposite conversion: gives the 3D coordinates {x, y, z} corresponding to the screen coordinates {sx, sy, sz}:
		+	point({sx,sy,sz}, false);
		+	Example of use:
		+	<pre>
		+	p4 = point( {124, -230, 5000}, false)
		+	print p4.x;
		+	print p4.y;
		+	</pre>

@@ Line 3: / Line 3: @@
 When a file is loaded, the model contains a 3D space system of coordinates and the values of x,y,z for every atom. This coordinate system is inherent to the model. If you load several models, each one brings its own coordinates, so you will usually see both models positioned very far apart, or sometimes overlapping.
-Jmol uses this 3D coordinates for all the operations.
+Some commands, however, refer to a 2D space, the projection that the observer sees; these are the "screen coordinates".
-Some commands, however, refer to a 2D space, the projection that the observer sees; these are the "screen coordinates".
+Jmol uses these 3D coordinates for all the operations. Note also that, when the model is rotated or translated (either by mouse action or by commands) the coordinate system and axes move together with the model. That is, position of the model in the 3D coordinate system is always the same; it's just the viewpoint that changes (and, accordingly, the screen coordinates do change with any rotation, translation or zoom).
 === Retrieving 3D coordinates ===
-The position of the origin and the orientation of the x,y,z axes may be anyone with respect to the viewer (i.e. the screen display) when a model file is loaded. The command <code>axes on</code> will let you check those.
+When a model file is loaded, the position of the origin and the orientation of the x,y,z axes are usually:
 Examples of how to check the coordinates of an atom: