Molecular replacement - Revision history

Kay: /* Self-rotation function */

2011-08-30T07:34:54Z

Self-rotation function

← Older revision		Revision as of 09:34, 30 August 2011
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	A self-rotation function may be calculated and visualized with the help of [[molrep]] or [[polarrfn]].		A self-rotation function may be calculated and visualized with the help of [[molrep]] or [[polarrfn]].

			Details can be found at [http://www.ccp4.ac.uk/dist/ccp4i/help/modules/appendices/mr-bathtutorial/mrbath2.html#section2.8] (and the following section 2.9) and at [http://www.ccp4.ac.uk/dist/ccp4i/help/modules/appendices/mr-bathtutorial/mrbath5.html] (see section 5.2).

	== Rotation function (RF) ==		== Rotation function (RF) ==

Kay: /* Self-rotation function */

2008-04-24T10:42:27Z

Self-rotation function

← Older revision		Revision as of 12:42, 24 April 2008
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	== Self-rotation function ==		== Self-rotation function ==

	A self-rotation function may be calculated to find the relative rotation between two molecules in the asymmetric unit. It is often calculated in polar coordinates (phi~~, psi~~, kappa), because these separate the amount of rotation (kappa) from the axis around which the rotation takes place (phi, ~~psi~~).		A self-rotation function may be calculated to find the relative rotation between two molecules in the asymmetric unit. It is often calculated in polar coordinates (theta, phi, kappa), because these separate the amount of rotation (kappa) from the axis around which the rotation takes place (theta, phi) (called omega, phi in the [http://www.ccp4.ac.uk/html/polarrfn.html polarrfn documentation]).

	For visualization often a [[stereographic projection]] is used.		For visualization often a [[stereographic projection]] is used.

			A self-rotation function may be calculated and visualized with the help of [[molrep]] or [[polarrfn]].

	== Rotation function (RF) ==		== Rotation function (RF) ==

Kay at 10:31, 24 April 2008

2008-04-24T10:31:52Z

← Older revision		Revision as of 12:31, 24 April 2008
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	The intra-molecular vectors would change their orientation (but not their length) when the molecule of the ASU would rotate. For a given rotation of that molecule, only the inter-molecular vectors would change upon translation of the molecule through the ASU.		The intra-molecular vectors would change their orientation (but not their length) when the molecule of the ASU would rotate. For a given rotation of that molecule, only the inter-molecular vectors would change upon translation of the molecule through the ASU.
	It is thus clear that it is advantageous to first determine the rotation of the molecule, by restricting the comparison between model patterson and crystal patterson to the intra-molecular vectors. When the correct rotation is found, all vectors may then be used to find the correct translation.		It is thus clear that it is advantageous to first determine the rotation of the molecule, by restricting the comparison between model patterson and crystal patterson to the intra-molecular vectors. When the correct rotation is found, all vectors may then be used to find the correct translation.

			== Self-rotation function ==

			A self-rotation function may be calculated to find the relative rotation between two molecules in the asymmetric unit. It is often calculated in polar coordinates (phi, psi, kappa), because these separate the amount of rotation (kappa) from the axis around which the rotation takes place (phi, psi).

			For visualization often a [[stereographic projection]] is used.

	== Rotation function (RF) ==		== Rotation function (RF) ==

Kay at 07:21, 1 April 2008

2008-04-01T07:21:14Z

← Older revision		Revision as of 09:21, 1 April 2008
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	Molecular replacement serves to position one or more known structures (models) in the unit cell of the unknown crystal structure with the goal of providing preliminary phase information.		Molecular replacement serves to position one or more known structures (models) in the unit cell of the unknown crystal structure with the goal of providing preliminary phase information.

			For the positioning of a single molecule in the asymmetric unit (ASU), there are 6 degrees of freedom: 3 d.o.f. for rotation (around e.g. the x, y, and z axes), and 3 d.o.f. for translation along (e.g.) x,y,z.

			A 6-dimensional search is computationally very demanding if it is performed on a suitable grid. As an example, rotating on a 3-dimensional grid with 10° spacing means almost 14000 unique possibilities (using [[Lattman angles]]); a more exhaustive 5° search would mean 8 times as many possibilities. Translating on a 3-dimensional grid with 1 Å spacing in a 100 * 100 * 100 Å^3 unit cell means 1.000.000 translations. Doing both (a translation search for each rotation, or ''vice versa'') then would lead to a combinatorial explosion of the number of possibilites that have to be evaluated.

			It was recognized by Rossmann and Blow (around 1962) (FIXME: give correct reference) that a Patterson function can conceptually be decomposed into those vectors arising from intra-molecular vectors, and those from inter-molecular vectors.
			The intra-molecular vectors would change their orientation (but not their length) when the molecule of the ASU would rotate. For a given rotation of that molecule, only the inter-molecular vectors would change upon translation of the molecule through the ASU.
			It is thus clear that it is advantageous to first determine the rotation of the molecule, by restricting the comparison between model patterson and crystal patterson to the intra-molecular vectors. When the correct rotation is found, all vectors may then be used to find the correct translation.

			== Rotation function (RF) ==
			=== Fast rotation function (FRF) ===
			=== scoring functions ===

			== Translation function ==
			=== Fast translation function ===
			=== scoring functions ===

	== Molecular Replacement Programs ==		== Molecular Replacement Programs ==

Kay: /* Molecular Replacment Programs */

2008-04-01T06:58:30Z

Molecular Replacment Programs

← Older revision		Revision as of 08:58, 1 April 2008
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	Molecular replacement serves to position one or more known structures (models) in the unit cell of the unknown crystal structure with the goal of providing preliminary phase information.		Molecular replacement serves to position one or more known structures (models) in the unit cell of the unknown crystal structure with the goal of providing preliminary phase information.

	== Molecular ~~Replacment~~ Programs ==		== Molecular Replacement Programs ==

	* PHASER		* [[PHASER]]
	* MOLREP		* [[MOLREP]]
	* AMORE		* [[AMORE]]
	* CNS		* [[CNS]]
	* EPMR		* [[EPMR]]
	* BEAST		* BEAST - Fortran77 precursor of [[PHASER]]; withdrawn as of CCP4 6.1
	* GLRF		* [[GLRF]]
	* NORMA		* NORMA
	* Qs		* Qs

Panjikar at 09:13, 7 March 2008

2008-03-07T09:13:37Z

← Older revision		Revision as of 11:13, 7 March 2008
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	Molecular replacement serves to position one or more known structures (models) in the unit cell of the unknown crystal structure with the goal of providing preliminary phase information.		Molecular replacement serves to position one or more known structures (models) in the unit cell of the unknown crystal structure with the goal of providing preliminary phase information.

			== Molecular Replacment Programs ==

			* PHASER
			* MOLREP
			* AMORE
			* CNS
			* EPMR
			* BEAST
			* GLRF
			* NORMA
			* Qs

3ND03P: Molecular replacement (MR) moved to Molecular replacement

2008-02-12T10:16:18Z

Molecular replacement (MR) moved to Molecular replacement

← Older revision	Revision as of 12:16, 12 February 2008
(No difference)

3ND03P: New page: Molecular replacement serves to position one or more known structures (models) in the unit cell of the unknown crystal structure with the goal of providing preliminary phase information.

2008-02-12T10:16:04Z

New page: Molecular replacement serves to position one or more known structures (models) in the unit cell of the unknown crystal structure with the goal of providing preliminary phase information.

New page

Molecular replacement serves to position one or more known structures (models) in the unit cell of the unknown crystal structure with the goal of providing preliminary phase information.