Temperature color schemes - Revision history

Eric Martz at 21:30, 25 July 2018

Eric Martz — Wed, 25 Jul 2018 21:30:21 GMT

←Older revision		Revision as of 21:30, 25 July 2018
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	==Jmol Scripts==		==Jmol Scripts==
-	The Jmol scripts used by the ''Temperature 0-10'' and ''Add 10'' buttons are:	+	The Jmol scripts used by the ''Temperature 0-10'' and ''Add 10'' buttons (below the table in the previous
		+	section) are:
	*[http://www.proteopedia.org/wiki/images/9/97/TempRangeReset.spt TempRangeReset.spt]		*[http://www.proteopedia.org/wiki/images/9/97/TempRangeReset.spt TempRangeReset.spt]
	*[http://www.proteopedia.org/wiki/images/2/28/TempRangeStep.spt TempRangeStep.spt]		*[http://www.proteopedia.org/wiki/images/2/28/TempRangeStep.spt TempRangeStep.spt]

Wayne Decatur: added color keys because searching for color has this page high in search results and not help color keys

Wayne Decatur — Tue, 12 May 2015 18:04:48 GMT

added color keys because searching for color has this page high in search results and not help color keys

←Older revision		Revision as of 18:04, 12 May 2015
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	set echo echotl 0% 100%;		set echo echotl 0% 100%;
	</pre>		</pre>
		+
		+	==See Also==
		+
		+	*[[Help:Color Keys]]

Eric Martz at 22:13, 20 July 2011

Eric Martz — Wed, 20 Jul 2011 22:13:41 GMT

←Older revision		Revision as of 22:13, 20 July 2011
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	'''Relative Temperature Color Scheme (''Limited Value/Misleading'')'''		'''Relative Temperature Color Scheme (''Limited Value/Misleading'')'''
	{{Template:ColorKey_TemperatureRelative}}		{{Template:ColorKey_TemperatureRelative}}
-	</center>
	([[Help:Color_Keys#Temperature_Value\|Instructions]] for inserting the above color keys		([[Help:Color_Keys#Temperature_Value\|Instructions]] for inserting the above color keys
	into Proteopedia articles.)		into Proteopedia articles.)
		+	</center>

	*The '''fixed (absolute)''' color scheme is by far the most informative, because colors are mapped to the absolute temperature values themselves. It enables valid comparisions to be made between different models ([[PDB files]]).		*The '''fixed (absolute)''' color scheme is by far the most informative, because colors are mapped to the absolute temperature values themselves. It enables valid comparisions to be made between different models ([[PDB files]]).

Eric Martz at 22:12, 20 July 2011

Eric Martz — Wed, 20 Jul 2011 22:12:23 GMT

←Older revision		Revision as of 22:12, 20 July 2011
Line 10:		Line 10:
	{{Template:ColorKey_TemperatureRelative}}		{{Template:ColorKey_TemperatureRelative}}
	</center>		</center>
		+	([[Help:Color_Keys#Temperature_Value\|Instructions]] for inserting the above color keys
		+	into Proteopedia articles.)

	*The '''fixed (absolute)''' color scheme is by far the most informative, because colors are mapped to the absolute temperature values themselves. It enables valid comparisions to be made between different models ([[PDB files]]).		*The '''fixed (absolute)''' color scheme is by far the most informative, because colors are mapped to the absolute temperature values themselves. It enables valid comparisions to be made between different models ([[PDB files]]).

Eric Martz at 23:25, 8 July 2011

Eric Martz — Fri, 08 Jul 2011 23:25:21 GMT

←Older revision		Revision as of 23:25, 8 July 2011
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-	<font color="red">This article is under development and some assertions below ~~will probably~~ be toned down!</font>	+	<font color="red">This article is under development and some assertions below may eventually be toned down!</font>

	The [[temperature value]] represents the uncertainty in the position of an atom in a [[X-ray crystallography\|crystallographic]] model. Coloring each atom according to its temperature value makes it easy to see variations in the uncertainty of atomic positions throughout the model. This reveals local uncertainty whereas the [[Resolution]] represents the average uncertainty for the model.		The [[temperature value]] represents the uncertainty in the position of an atom in a [[X-ray crystallography\|crystallographic]] model. Coloring each atom according to its temperature value makes it easy to see variations in the uncertainty of atomic positions throughout the model. This reveals local uncertainty whereas the [[Resolution]] represents the average uncertainty for the model.

Eric Martz at 23:37, 27 June 2011

Eric Martz — Mon, 27 Jun 2011 23:37:46 GMT

←Older revision		Revision as of 23:37, 27 June 2011
Line 1:		Line 1:
		+	<font color="red">This article is under development and some assertions below will probably be toned down!</font>
		+
	The [[temperature value]] represents the uncertainty in the position of an atom in a [[X-ray crystallography\|crystallographic]] model. Coloring each atom according to its temperature value makes it easy to see variations in the uncertainty of atomic positions throughout the model. This reveals local uncertainty whereas the [[Resolution]] represents the average uncertainty for the model.		The [[temperature value]] represents the uncertainty in the position of an atom in a [[X-ray crystallography\|crystallographic]] model. Coloring each atom according to its temperature value makes it easy to see variations in the uncertainty of atomic positions throughout the model. This reveals local uncertainty whereas the [[Resolution]] represents the average uncertainty for the model.
	<center>		<center>

Eric Martz: /* Jmol Scripts */

Eric Martz — Mon, 27 Jun 2011 23:08:24 GMT

Jmol Scripts

←Older revision		Revision as of 23:08, 27 June 2011
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	<pre>		<pre>
	select all;		select all;
		+	color fixedTemperature;
	cartoon off;		cartoon off;
	spacefill off;		spacefill off;
-	wireframe 0.2 ~~only~~;	+	wireframe 0.2;
		+	select solvent;
		+	spacefill 0.5;
	background black;		background black;
	ssbonds off;		ssbonds off;
-	color fixedTemperature;

	hover Temp=%t, %n %R, Chain=%c, Element=%e(%a);		hover Temp=%t, %n %R, Chain=%c, Element=%e(%a);

Eric Martz at 23:03, 27 June 2011

Eric Martz — Mon, 27 Jun 2011 23:03:47 GMT

←Older revision		Revision as of 23:03, 27 June 2011
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	*The '''fixed (absolute)''' color scheme is by far the most informative, because colors are mapped to the absolute temperature values themselves. It enables valid comparisions to be made between different models ([[PDB files]]).		*The '''fixed (absolute)''' color scheme is by far the most informative, because colors are mapped to the absolute temperature values themselves. It enables valid comparisions to be made between different models ([[PDB files]]).
-	*The '''relative''' color scheme is of limited value. Because it gives no sense of the actual temperature values, it is misleading. Different models ([[PDB files]]) cannot be meaningfully compared using the relative color scheme. The only value of this color scheme is to make it easier to find the atoms with the highest temperature values. Using the fixed/absolute color scheme, these highest-temperature-atoms are difficult to see when the maximum temperature is below 50.	+	*The '''relative''' color scheme is of limited value. Because it gives no sense of the actual temperature values, it can be misleading. Different models ([[PDB files]]) cannot be meaningfully compared using the relative color scheme. The only value of this color scheme is to make it easier to find the atoms with the highest temperature values. Using the fixed/absolute color scheme, these highest-temperature-atoms are difficult to see when the maximum temperature is below 50.

	As the [[#Examples\|examples below]] illustrate, generally, the average temperature value in a [[X-ray crystallography\|crystallographic]] model goes up as the value of [[resolution]] goes up. For more data, please see [[Temperature value vs. resolution]].		As the [[#Examples\|examples below]] illustrate, generally, the average temperature value in a [[X-ray crystallography\|crystallographic]] model goes up as the value of [[resolution]] goes up. For more data, please see [[Temperature value vs. resolution]].

Eric Martz at 22:59, 27 June 2011

Eric Martz — Mon, 27 Jun 2011 22:59:31 GMT

←Older revision		Revision as of 22:59, 27 June 2011
Line 10:		Line 10:

	*The '''fixed (absolute)''' color scheme is by far the most informative, because colors are mapped to the absolute temperature values themselves. It enables valid comparisions to be made between different models ([[PDB files]]).		*The '''fixed (absolute)''' color scheme is by far the most informative, because colors are mapped to the absolute temperature values themselves. It enables valid comparisions to be made between different models ([[PDB files]]).
-	*The '''relative''' color scheme is of limited value. Because it gives no sense of the actual temperature values, it is misleading. Different models ([[PDB files]]) cannot be meaningfully compared using the relative color scheme. The only value of this color scheme is to ~~quickly spot~~ the atoms with the highest temperature values. Using the fixed/absolute color scheme, these highest-temperature-atoms are difficult to see when the maximum temperature is ~~well~~ below 50.	+	*The '''relative''' color scheme is of limited value. Because it gives no sense of the actual temperature values, it is misleading. Different models ([[PDB files]]) cannot be meaningfully compared using the relative color scheme. The only value of this color scheme is to make it easier to find the atoms with the highest temperature values. Using the fixed/absolute color scheme, these highest-temperature-atoms are difficult to see when the maximum temperature is below 50.

	As the [[#Examples\|examples below]] illustrate, generally, the average temperature value in a [[X-ray crystallography\|crystallographic]] model goes up as the value of [[resolution]] goes up. For more data, please see [[Temperature value vs. resolution]].		As the [[#Examples\|examples below]] illustrate, generally, the average temperature value in a [[X-ray crystallography\|crystallographic]] model goes up as the value of [[resolution]] goes up. For more data, please see [[Temperature value vs. resolution]].

Eric Martz at 22:57, 27 June 2011

Eric Martz — Mon, 27 Jun 2011 22:57:58 GMT

←Older revision		Revision as of 22:57, 27 June 2011
Line 1:		Line 1:
	The [[temperature value]] represents the uncertainty in the position of an atom in a [[X-ray crystallography\|crystallographic]] model. Coloring each atom according to its temperature value makes it easy to see variations in the uncertainty of atomic positions throughout the model. This reveals local uncertainty whereas the [[Resolution]] represents the average uncertainty for the model.		The [[temperature value]] represents the uncertainty in the position of an atom in a [[X-ray crystallography\|crystallographic]] model. Coloring each atom according to its temperature value makes it easy to see variations in the uncertainty of atomic positions throughout the model. This reveals local uncertainty whereas the [[Resolution]] represents the average uncertainty for the model.
	<center>		<center>
-	'''Fixed (Absolute) Temperature Color Scheme'''	+	'''Fixed (Absolute) Temperature Color Scheme (''Recommended'')'''
	{{Template:ColorKey_TemperatureFixed}}		{{Template:ColorKey_TemperatureFixed}}


-	'''Relative Temperature Color Scheme'''	+	'''Relative Temperature Color Scheme (''Limited Value/Misleading'')'''
	{{Template:ColorKey_TemperatureRelative}}		{{Template:ColorKey_TemperatureRelative}}
	</center>		</center>