Advanced colouring - Revision history

import>Khs26: Fixed formatting again, 'cause I'm useless with Wiki editing.

2008-08-21T09:47:53Z

Fixed formatting again, 'cause I'm useless with Wiki editing.

← Older revision		Revision as of 09:47, 21 August 2008
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	The list of possible spectra (from the PyMolWiki) is:		The list of possible spectra (from the PyMolWiki) is:
	blue_green, green_white_magenta, red_cyan, blue_magenta, green_white_red, red_green, blue_red, green_white_yellow, red_white_blue, blue_white_green, green_yellow, red_white_cyan, blue_white_magenta,		blue_green, green_white_magenta, red_cyan, blue_magenta, green_white_red, red_green, blue_red, green_white_yellow, red_white_blue, blue_white_green, green_yellow, red_white_cyan, blue_white_magenta,
	green_yellow_red, red_white_green, blue_white_red, magenta_blue, red_white_yellow, blue_white_yellow, magenta_cyan, red_yellow, blue_yellow, magenta_green, red_yellow_green, cbmr,		green_yellow_red, red_white_green, blue_white_red, magenta_blue, red_white_yellow, blue_white_yellow, magenta_cyan, red_yellow, blue_yellow, magenta_green, red_yellow_green, cbmr,
	magenta_white_blue, rmbc, cyan_magenta, magenta_white_cyan, yellow_blue, cyan_red, magenta_white_green, yellow_cyan, cyan_white_magenta, magenta_white_yellow, yellow_cyan_white, cyan_white_red,		magenta_white_blue, rmbc, cyan_magenta, magenta_white_cyan, yellow_blue, cyan_red, magenta_white_green, yellow_cyan, cyan_white_magenta, magenta_white_yellow, yellow_cyan_white, cyan_white_red,
	magenta_yellow, yellow_green, cyan_white_yellow, rainbow, yellow_magenta, cyan_yellow, rainbow2, yellow_red, gcbmry, rainbow2_rev, yellow_white_blue, green_blue, rainbow_cycle, yellow_white_green,		magenta_yellow, yellow_green, cyan_white_yellow, rainbow, yellow_magenta, cyan_yellow, rainbow2, yellow_red, gcbmry, rainbow2_rev, yellow_white_blue, green_blue, rainbow_cycle, yellow_white_green,
	green_magenta, rainbow_cycle_rev, yellow_white_magenta, green_red, rainbow_rev, yellow_white_red, green_white_blue, red_blue, yrmbcg		green_magenta, rainbow_cycle_rev, yellow_white_magenta, green_red, rainbow_rev, yellow_white_red, green_white_blue, red_blue, yrmbcg

import>Khs26: Formatting

2008-08-21T09:47:16Z

Formatting

← Older revision		Revision as of 09:47, 21 August 2008
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	The list of possible spectra (from the PyMolWiki) is:		The list of possible spectra (from the PyMolWiki) is:
	blue_green, green_white_magenta, red_cyan, blue_magenta, green_white_red, red_green, blue_red, green_white_yellow, red_white_blue, blue_white_green, green_yellow, red_white_cyan, blue_white_magenta, green_yellow_red, red_white_green, blue_white_red, magenta_blue, red_white_yellow, blue_white_yellow, magenta_cyan, red_yellow, blue_yellow, magenta_green, red_yellow_green, cbmr, magenta_white_blue, rmbc, cyan_magenta, magenta_white_cyan, yellow_blue, cyan_red, magenta_white_green, yellow_cyan, cyan_white_magenta, magenta_white_yellow, yellow_cyan_white, cyan_white_red, magenta_yellow, yellow_green, cyan_white_yellow, rainbow, yellow_magenta, cyan_yellow, rainbow2, yellow_red, gcbmry, rainbow2_rev, yellow_white_blue, green_blue, rainbow_cycle, yellow_white_green, green_magenta, rainbow_cycle_rev, yellow_white_magenta, green_red, rainbow_rev, yellow_white_red, green_white_blue, red_blue, yrmbcg		blue_green, green_white_magenta, red_cyan, blue_magenta, green_white_red, red_green, blue_red, green_white_yellow, red_white_blue, blue_white_green, green_yellow, red_white_cyan, blue_white_magenta,
			green_yellow_red, red_white_green, blue_white_red, magenta_blue, red_white_yellow, blue_white_yellow, magenta_cyan, red_yellow, blue_yellow, magenta_green, red_yellow_green, cbmr,
			magenta_white_blue, rmbc, cyan_magenta, magenta_white_cyan, yellow_blue, cyan_red, magenta_white_green, yellow_cyan, cyan_white_magenta, magenta_white_yellow, yellow_cyan_white, cyan_white_red,
			magenta_yellow, yellow_green, cyan_white_yellow, rainbow, yellow_magenta, cyan_yellow, rainbow2, yellow_red, gcbmry, rainbow2_rev, yellow_white_blue, green_blue, rainbow_cycle, yellow_white_green,
			green_magenta, rainbow_cycle_rev, yellow_white_magenta, green_red, rainbow_rev, yellow_white_red, green_white_blue, red_blue, yrmbcg

import>Khs26 at 09:46, 21 August 2008

2008-08-21T09:46:47Z

← Older revision		Revision as of 09:46, 21 August 2008
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	The list of possible spectra (from the PyMolWiki) is:		The list of possible spectra (from the PyMolWiki) is:
		⚫	blue_green, green_white_magenta, red_cyan, blue_magenta, green_white_red, red_green, blue_red, green_white_yellow, red_white_blue, blue_white_green, green_yellow, red_white_cyan, blue_white_magenta, green_yellow_red, red_white_green, blue_white_red, magenta_blue, red_white_yellow, blue_white_yellow, magenta_cyan, red_yellow, blue_yellow, magenta_green, red_yellow_green, cbmr, magenta_white_blue, rmbc, cyan_magenta, magenta_white_cyan, yellow_blue, cyan_red, magenta_white_green, yellow_cyan, cyan_white_magenta, magenta_white_yellow, yellow_cyan_white, cyan_white_red, magenta_yellow, yellow_green, cyan_white_yellow, rainbow, yellow_magenta, cyan_yellow, rainbow2, yellow_red, gcbmry, rainbow2_rev, yellow_white_blue, green_blue, rainbow_cycle, yellow_white_green, green_magenta, rainbow_cycle_rev, yellow_white_magenta, green_red, rainbow_rev, yellow_white_red, green_white_blue, red_blue, yrmbcg
	<pre>

⚫	blue_green, green_white_magenta, red_cyan, blue_magenta, green_white_red, red_green, blue_red, green_white_yellow, red_white_blue, blue_white_green, green_yellow, red_white_cyan, blue_white_magenta, green_yellow_red, red_white_green, blue_white_red, magenta_blue, red_white_yellow, blue_white_yellow, magenta_cyan, red_yellow, blue_yellow, magenta_green, red_yellow_green, cbmr, magenta_white_blue, rmbc, cyan_magenta, magenta_white_cyan, yellow_blue, cyan_red, magenta_white_green, yellow_cyan, cyan_white_magenta, magenta_white_yellow, yellow_cyan_white, cyan_white_red, magenta_yellow, yellow_green, cyan_white_yellow, rainbow, yellow_magenta, cyan_yellow, rainbow2, yellow_red, gcbmry, rainbow2_rev, yellow_white_blue, green_blue, rainbow_cycle, yellow_white_green, green_magenta, rainbow_cycle_rev, yellow_white_magenta, green_red, rainbow_rev, yellow_white_red, green_white_blue, red_blue, yrmbcg
	</pre>

	'''NOTE: this will not work if you load in a .pdb as it does not contain charge information!'''		'''NOTE: this will not work if you load in a .pdb as it does not contain charge information!'''

import>Khs26: Added spectrum

2008-08-21T09:46:21Z

Added spectrum

← Older revision		Revision as of 09:46, 21 August 2008
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	</pre>		</pre>
	This shades atoms in the selection (object) ''''all''' in a spectrum from red, through white, to blue - by the value of '''pc.'''.		This shades atoms in the selection (object) ''''all''' in a spectrum from red, through white, to blue - by the value of '''pc.'''.

			The list of possible spectra (from the PyMolWiki) is:
			<pre>
			blue_green, green_white_magenta, red_cyan, blue_magenta, green_white_red, red_green, blue_red, green_white_yellow, red_white_blue, blue_white_green, green_yellow, red_white_cyan, blue_white_magenta, green_yellow_red, red_white_green, blue_white_red, magenta_blue, red_white_yellow, blue_white_yellow, magenta_cyan, red_yellow, blue_yellow, magenta_green, red_yellow_green, cbmr, magenta_white_blue, rmbc, cyan_magenta, magenta_white_cyan, yellow_blue, cyan_red, magenta_white_green, yellow_cyan, cyan_white_magenta, magenta_white_yellow, yellow_cyan_white, cyan_white_red, magenta_yellow, yellow_green, cyan_white_yellow, rainbow, yellow_magenta, cyan_yellow, rainbow2, yellow_red, gcbmry, rainbow2_rev, yellow_white_blue, green_blue, rainbow_cycle, yellow_white_green, green_magenta, rainbow_cycle_rev, yellow_white_magenta, green_red, rainbow_rev, yellow_white_red, green_white_blue, red_blue, yrmbcg
			</pre>

	'''NOTE: this will not work if you load in a .pdb as it does not contain charge information!'''		'''NOTE: this will not work if you load in a .pdb as it does not contain charge information!'''

import>Khs26: Moved the . and added emphasis

2008-08-21T09:44:58Z

Moved the . and added emphasis

← Older revision		Revision as of 09:44, 21 August 2008
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	load min1.rst , OTVresp		load min1.rst , OTVresp
	</pre>		</pre>
	You should now see both structures. Once you have altered their appearance to your satisfaction, you need to do the colouring. Partial charge is contained in the '''.pc''' array. For example, you can select all atoms with partial charge greater than 0.1 using:		You should now see both structures. Once you have altered their appearance to your satisfaction, you need to do the colouring. Partial charge is contained in the '''pc.''' array (N.B. the . character '''must''' be present). For example, you can select all atoms with partial charge greater than 0.1 using:
	<pre>		<pre>
	sele pc. > 0.1		sele pc. > 0.1

import>Mp466 at 22:01, 20 August 2008

2008-08-20T22:01:24Z

← Older revision		Revision as of 22:01, 20 August 2008
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	'''NOTE: this will not work if you load in a .pdb as it does not contain charge information!'''		'''NOTE: this will not work if you load in a .pdb as it does not contain charge information!'''

			There probably is a way around this with a pdb file. The pdb files can be colored on a residue by residue basis by using the temperature factor field.

import>Csw34 at 11:13, 20 August 2008

2008-08-20T11:13:01Z

← Older revision		Revision as of 11:13, 20 August 2008
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	</pre>		</pre>
	This shades atoms in the selection (object) ''''all''' in a spectrum from red, through white, to blue - by the value of '''pc.'''.		This shades atoms in the selection (object) ''''all''' in a spectrum from red, through white, to blue - by the value of '''pc.'''.

			'''NOTE: this will not work if you load in a .pdb as it does not contain charge information!'''

import>Csw34 at 11:12, 20 August 2008

2008-08-20T11:12:26Z

← Older revision		Revision as of 11:12, 20 August 2008
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	You can do all sorts of weird and wonderful colouring with Pymol - but the syntax is slightly cryptic. You can find some examples on the Pymol Wiki [http://www.pymolwiki.org/index.php/Color here] and [http://www.pymolwiki.org/index.php/Advanced_Coloring here].		You can do all sorts of weird and wonderful colouring with [[Pymol]] - but the syntax is slightly cryptic. You can find some examples on the Pymol Wiki [http://www.pymolwiki.org/index.php/Color here] and [http://www.pymolwiki.org/index.php/Advanced_Coloring here].

	=== Shading with a spectrum representing an atomic property ===		=== Shading with a spectrum representing an atomic property ===

	Say you have the AMBER topology files for a small drug molecule which has been parametrised in two different ways, and you would like to compare the partial atomic charges on each molecule. For this example. there are three files required - OTV_bcc.top and OTV_resp.top are actually [[AMBER]] .prmtop files. I have renamed them .top as this is what Pymol expects. You can force a file format with the load command however. Finally, min1.rst is an amber coordinate file. If you have problems using .rst files, compare them to an equivalent .inpcrd file and check the spacing.		Say you have the [[AMBER]] topology files for a small drug molecule which has been parametrised in two different ways, and you would like to compare the partial atomic charges on each molecule. For this example. there are three files required - OTV_bcc.top and OTV_resp.top are actually [[AMBER]] .prmtop files. I have renamed them .top as this is what [[Pymol]] expects. You can force a file format with the load command however. Finally, min1.rst is an amber coordinate file. If you have problems using .rst files, compare them to an equivalent .inpcrd file and check the spacing.

	Firstly - you'll need to load the structures into Pymol. For topology files, you first need to define the topology object, and then load the coordinates in.		Firstly - you'll need to load the structures into Pymol. For topology files, you first need to define the topology object, and then load the coordinates in.

import>Csw34 at 11:11, 20 August 2008

2008-08-20T11:11:59Z

← Older revision		Revision as of 11:11, 20 August 2008
Line 1:		Line 1:
	You can do all sorts of weird and wonderful colouring with Pymol - but the syntax is slightly cryptic. You can find some examples on the Pymol Wiki [http://www.pymolwiki.org/index.php/Color here] and [http://www.pymolwiki.org/index.php/Advanced_Coloring here].		You can do all sorts of weird and wonderful colouring with Pymol - but the syntax is slightly cryptic. You can find some examples on the Pymol Wiki [http://www.pymolwiki.org/index.php/Color here] and [http://www.pymolwiki.org/index.php/Advanced_Coloring here].

	=== Shading in a spectrum representing an atomic property ===		=== Shading with a spectrum representing an atomic property ===

	Say you have the AMBER topology files for a small drug molecule which has been parametrised in two different ways, and you would like to compare the partial atomic charges on each molecule. For this example. there are three files required - OTV_bcc.top and OTV_resp.top are actually [[AMBER]] .prmtop files. I have renamed them .top as this is what Pymol expects. You can force a file format with the load command however. Finally, min1.rst is an amber coordinate file. If you have problems using .rst files, compare them to an equivalent .inpcrd file and check the spacing.		Say you have the AMBER topology files for a small drug molecule which has been parametrised in two different ways, and you would like to compare the partial atomic charges on each molecule. For this example. there are three files required - OTV_bcc.top and OTV_resp.top are actually [[AMBER]] .prmtop files. I have renamed them .top as this is what Pymol expects. You can force a file format with the load command however. Finally, min1.rst is an amber coordinate file. If you have problems using .rst files, compare them to an equivalent .inpcrd file and check the spacing.

import>Csw34 at 11:11, 20 August 2008

2008-08-20T11:11:42Z

← Older revision		Revision as of 11:11, 20 August 2008
Line 1:		Line 1:
	You can do all sorts of weird and wonderful colouring with Pymol - but the syntax is slightly cryptic. You can find some examples on the Pymol Wiki [http://www.pymolwiki.org/index.php/Color here] and [http://www.pymolwiki.org/index.php/Advanced_Coloring here].		You can do all sorts of weird and wonderful colouring with Pymol - but the syntax is slightly cryptic. You can find some examples on the Pymol Wiki [http://www.pymolwiki.org/index.php/Color here] and [http://www.pymolwiki.org/index.php/Advanced_Coloring here].

			=== Shading in a spectrum representing an atomic property ===
⚫	As an example - say you have the AMBER topology files for a small drug molecule which has been parametrised in two different ways, and you would like to compare the partial atomic charges on each molecule. Firstly - you'll need to load the structures into Pymol. For topology files, you first need to define the topology object, and then load the coordinates in.

			Say you have the AMBER topology files for a small drug molecule which has been parametrised in two different ways, and you would like to compare the partial atomic charges on each molecule. For this example. there are three files required - OTV_bcc.top and OTV_resp.top are actually [[AMBER]] .prmtop files. I have renamed them .top as this is what Pymol expects. You can force a file format with the load command however. Finally, min1.rst is an amber coordinate file. If you have problems using .rst files, compare them to an equivalent .inpcrd file and check the spacing.

		⚫	Firstly - you'll need to load the structures into Pymol. For topology files, you first need to define the topology object, and then load the coordinates in.

	Defining the topology object for each:		Defining the topology object for each: