RDC Refinement with XPLOR-NIH - Revision history

Hlee at 19:28, 5 April 2012

2012-04-05T19:28:46Z

← Older revision		Revision as of 19:28, 5 April 2012
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	::- Backbone hydrogen bonding database (Optional)		::- Backbone hydrogen bonding database (Optional)

	<br>		<br>

	=== Getting Started ===		=== Getting Started ===
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	assign ( resid 2 and name HA ) ( resid 2 and name HG1 ) 4.00 2.20 1.00		assign ( resid 2 and name HA ) ( resid 2 and name HG1 ) 4.00 2.20 1.00
	assign ( resid 2 and name HA ) ( resid 2 and name HE* ) 4.00 2.20 1.00		assign ( resid 2 and name HA ) ( resid 2 and name HE* ) 4.00 2.20 1.00
	</pre>		</pre>

	==== Dihedral Angle Table ====		==== Dihedral Angle Table ====

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	assign ( resid 7 and name C ) ( resid 8 and name N )		assign ( resid 7 and name C ) ( resid 8 and name N )
	(resid 8 and name CA ) ( resid 8 and name C ) 1 -71.00 34.00 2 # For Psi Angle		(resid 8 and name CA ) ( resid 8 and name C ) 1 -71.00 34.00 2 # For Psi Angle
	</pre>		</pre>

	==== RDC Table ====		==== RDC Table ====

	An example of the RDC table in XPLOR format is shown below:		An example of the RDC table in XPLOR format is shown below:

	:'''( resid 500 and name OO )''': resid 500 is the residue number for the tensor axis system		:'''( resid 500 and name OO )''': resid 500 is the residue number for the tensor axis system
	:'''( resid # and name N )''': defines the first atom of the pair		:'''( resid # and name N )''': defines the first atom of the pair
	:'''( resid # and name HN ) 2.586 1.5''': defines the second atom of the pair, RDC_value, Error_value		:'''( resid # and name HN ) 2.586 1.5''': defines the second atom of the pair, RDC_value, Error_value
	::'''Note''': The error_value term is not utilized with the square potential of this script.		::'''Note''': The error_value term is not utilized with the square potential of this script.
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	( resid 3 and name C )		( resid 3 and name C )
	( resid 4 and name N ) -3.9435 1.5		( resid 4 and name N ) -3.9435 1.5
	</pre>		</pre>

	==== RCSA Restraint Table ====		==== RCSA Restraint Table ====

	An example of the RCSA table in XPLOR format is shown below:		An example of the RCSA table in XPLOR format is shown below:

	RCSAs can also be used to validate protein structure using [[REDCAT\|REDCAT]].		RCSAs can also be used to validate protein structure using [[REDCAT\|REDCAT]].

	Unlike RDCs which are defined with a single vector, RCSAs require a full 3 axis system. This is usually defined by identifying a set of 3 bonded atoms.		Unlike RDCs which are defined with a single vector, RCSAs require a full 3 axis system. This is usually defined by identifying a set of 3 bonded atoms.

	:'''(resid 2 and name C) (resid 3 and name N) (resid 3 and name HN) 29.040 24.750''': 29.040 is the N RCSA shift in PPB unit and 24.750 is a constant		:'''(resid 2 and name C) (resid 3 and name N) (resid 3 and name HN) 29.040 24.750''': 29.040 is the N RCSA shift in PPB unit and 24.750 is a constant
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	assign (resid 500 and name OO ) (resid 500 and name Z) (resid 500 and name X ) (resid 500 and name Y )		assign (resid 500 and name OO ) (resid 500 and name Z) (resid 500 and name X ) (resid 500 and name Y )
	(resid 8 and name C) (resid 8 and name O) (resid 9 and name N) -8.400 13.333		(resid 8 and name C) (resid 8 and name O) (resid 9 and name N) -8.400 13.333
	</pre>		</pre>

	=== Protocol for Inclusion of RDCs in Structure Determination ===		=== Protocol for Inclusion of RDCs in Structure Determination ===

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	IVM_groupRigidBackbone(minc)		IVM_groupRigidBackbone(minc)
	</pre>		</pre>

			=== Validation of Structures Using RDCs and RCSAs ===

Hlee at 19:26, 5 April 2012

2012-04-05T19:26:10Z

← Older revision		Revision as of 19:26, 5 April 2012
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	=== Protocol for Inclusion of RDCs in Structure Determination ===		=== Protocol for Inclusion of RDCs in Structure Determination ===

	~~It is easy to implement the RDC restraint using example simulated annealing protocol included in the Xplor distribution packages.~~ It is important to run more than one simulate annealing cycle (sometimes call annealing and refinement cycle). It is also important to recognized that RDCs error functions have multi-minimia and are not very useful in finding a suitable structure beginning far far away from the target. So RDCs are typically used in conduction with NOE data. In simulated annealing, the relative weight of RDCs data are low compare to weight of NOE at early point in the annealing protocol. The weight for both RDCs and NOEs are ramped up as temperature decreases, but the RDCs weight is ramp up more rapidly. In the scripts below, suggested starting for weighting factors are given. Note, in the case of multiple RDCs sets, additional relative weighting factors are given in proportion to the importance (size) of the varies RDCs. Ideally, weights are adjusted to produce Q-factor for back-calculated sets in the 0.1 to 0.2 ranges. Values below 0.1 are not normally justify by the quality of the data and may distort local bond geometry.		It is important to run more than one simulate annealing cycle (sometimes call annealing and refinement cycle). It is also important to recognized that RDCs error functions have multi-minimia and are not very useful in finding a suitable structure beginning far far away from the target. So RDCs are typically used in conduction with NOE data. In simulated annealing, the relative weight of RDCs data are low compare to weight of NOE at early point in the annealing protocol. The weight for both RDCs and NOEs are ramped up as temperature decreases, but the RDCs weight is ramp up more rapidly. In the scripts below, suggested starting for weighting factors are given. Note, in the case of multiple RDCs sets, additional relative weighting factors are given in proportion to the importance (size) of the varies RDCs. Ideally, weights are adjusted to produce Q-factor for back-calculated sets in the 0.1 to 0.2 ranges. Values below 0.1 are not normally justify by the quality of the data and may distort local bond geometry.

	<br> First, obtain a good estimate of the magnitude of Da and R from alignment tensors using either [[REDCAT\|REDCAT]] or PALES program and use this as a starting point for the refinement. Then edit the following portion of the refine.py script. Note: text on the same line and following a “#” sign is not read by the XPLOR program.		<br> First, obtain a good estimate of the magnitude of Da and R from alignment tensors using either [[REDCAT\|REDCAT]] or PALES program and use this as a starting point for the refinement. Then edit the following portion of the refine.py script. Note: text on the same line and following a “#” sign is not read by the XPLOR program.

Hlee at 19:25, 5 April 2012

2012-04-05T19:25:45Z

← Older revision		Revision as of 19:25, 5 April 2012
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	:Error correction of NOE, dihedral angle, RDCs, and RCSAs restraint		:Error correction of NOE, dihedral angle, RDCs, and RCSAs restraint

	<br> It is easy to implement the RDC ~~restraint~~ using example simulated annealing protocol included in the Xplor distribution packages~~. Here, we describe the RDCs and RCSAs refinement protocol using XPLOR-NIH~~. The python version of the refinement script was taken from the example dataset (xplor-nih-2.28/eginput/gb1_rdc/refine.py) provided by the XPLOR-NIH package (http://nmr.cit.nih.gov/xplor-nih/). The features of particular relevance to RDC refinement are as follows:		<br> It is easy to implement the RDC and RCSA restraints using example simulated annealing protocol included in the Xplor-NIH distribution packages. The python version of the refinement script was taken from the example dataset (xplor-nih-2.28/eginput/gb1_rdc/refine.py) provided by the XPLOR-NIH package (http://nmr.cit.nih.gov/xplor-nih/). The features of particular relevance to RDC refinement are as follows:
	<div></div>		<div></div>
	:- Variable tensor tools for floating the principal alignment parameters, Da and R, during refinement		:- Variable tensor tools for floating the principal alignment parameters, Da and R, during refinement

Hlee at 19:24, 5 April 2012

2012-04-05T19:24:19Z

← Older revision		Revision as of 19:24, 5 April 2012
Line 14:		Line 14:
	:Error correction of NOE, dihedral angle, RDCs, and RCSAs restraint		:Error correction of NOE, dihedral angle, RDCs, and RCSAs restraint

	<br> Here, we describe the RDCs and RCSAs refinement protocol using XPLOR-NIH. The python version of the refinement script was taken from the example dataset (xplor-nih-2.28/eginput/gb1_rdc/refine.py) provided by the XPLOR-NIH package (http://nmr.cit.nih.gov/xplor-nih/). The features of particular relevance to RDC refinement are as follows:		<br> It is easy to implement the RDC restraint using example simulated annealing protocol included in the Xplor distribution packages. Here, we describe the RDCs and RCSAs refinement protocol using XPLOR-NIH. The python version of the refinement script was taken from the example dataset (xplor-nih-2.28/eginput/gb1_rdc/refine.py) provided by the XPLOR-NIH package (http://nmr.cit.nih.gov/xplor-nih/). The features of particular relevance to RDC refinement are as follows:
	<div></div>		<div></div>
	:- Variable tensor tools for floating the principal alignment parameters, Da and R, during refinement		:- Variable tensor tools for floating the principal alignment parameters, Da and R, during refinement
	:- ?Database potentials of mean force to refine against?:		:- ?Database potentials of mean force to refine against?:
	::- Multidimensional torsion angles		::- Multidimensional torsion angles
	::- Backbone hydrogen bonding database (Optional)		::- Backbone hydrogen bonding database (Optional)

Hlee at 19:20, 5 April 2012

2012-04-05T19:20:44Z

← Older revision		Revision as of 19:20, 5 April 2012
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	=== Protocol for Inclusion of RDCs in Structure Determination ===		=== Protocol for Inclusion of RDCs in Structure Determination ===

	It is important to recognized that RDCs error functions have multi-minimia and are not very useful in finding a suitable structure beginning far far away from the target. So RDCs are typically used in conduction with NOE data. In simulated annealing, the relative weight of RDCs data are low compare to weight of NOE at early point in the annealing protocol. The weight for both RDCs and NOEs are ramped up as temperature decreases, but the RDCs weight is ramp up more rapidly. In the scripts below, suggested starting for weighting factors are given. Note, in the case of multiple RDCs sets, additional relative weighting factors are given in proportion to the importance (size) of the varies RDCs. Ideally, weights are adjusted to produce Q-factor for back-calculated sets in the 0.1 to 0.2 ranges. Values below 0.1 are not normally justify by the quality of the data and may distort local bond geometry.		It is easy to implement the RDC restraint using example simulated annealing protocol included in the Xplor distribution packages. It is important to run more than one simulate annealing cycle (sometimes call annealing and refinement cycle). It is also important to recognized that RDCs error functions have multi-minimia and are not very useful in finding a suitable structure beginning far far away from the target. So RDCs are typically used in conduction with NOE data. In simulated annealing, the relative weight of RDCs data are low compare to weight of NOE at early point in the annealing protocol. The weight for both RDCs and NOEs are ramped up as temperature decreases, but the RDCs weight is ramp up more rapidly. In the scripts below, suggested starting for weighting factors are given. Note, in the case of multiple RDCs sets, additional relative weighting factors are given in proportion to the importance (size) of the varies RDCs. Ideally, weights are adjusted to produce Q-factor for back-calculated sets in the 0.1 to 0.2 ranges. Values below 0.1 are not normally justify by the quality of the data and may distort local bond geometry.

			<br> First, obtain a good estimate of the magnitude of Da and R from alignment tensors using either [[REDCAT\|REDCAT]] or PALES program and use this as a starting point for the refinement. Then edit the following portion of the refine.py script. Note: text on the same line and following a “#” sign is not read by the XPLOR program.
	First, obtain a good estimate of the magnitude of Da and R from alignment tensors using either [[REDCAT\|REDCAT]] or PALES program and use this as a starting point for the refinement. Then edit the following portion of the refine.py script. Note: text on the same line and following a “#” sign is not read by the XPLOR program.

	:'''('t', -6.5, 0.62)''': this line refers to the Da and rhombicity for alignment medium t		:'''('t', -6.5, 0.62)''': this line refers to the Da and rhombicity for alignment medium t

Hlee at 19:14, 5 April 2012

2012-04-05T19:14:45Z

← Older revision		Revision as of 19:14, 5 April 2012
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	</pre>		</pre>

	=== Protocol for ~~RDC Refinement~~ ===		=== Protocol for Inclusion of RDCs in Structure Determination ===

	First, obtain a good estimate of the magnitude of Da and R from alignment tensors using either [[REDCAT\|REDCAT]] or PALES program and use this as a starting point for the refinement. Then edit the following portion of the refine.py script. Note: text on the same line and following a “#” sign is not read by the XPLOR program.		It is important to recognized that RDCs error functions have multi-minimia and are not very useful in finding a suitable structure beginning far far away from the target. So RDCs are typically used in conduction with NOE data. In simulated annealing, the relative weight of RDCs data are low compare to weight of NOE at early point in the annealing protocol. The weight for both RDCs and NOEs are ramped up as temperature decreases, but the RDCs weight is ramp up more rapidly. In the scripts below, suggested starting for weighting factors are given. Note, in the case of multiple RDCs sets, additional relative weighting factors are given in proportion to the importance (size) of the varies RDCs. Ideally, weights are adjusted to produce Q-factor for back-calculated sets in the 0.1 to 0.2 ranges. Values below 0.1 are not normally justify by the quality of the data and may distort local bond geometry.
	:'''('t', -6.5, 0.62)''': this line refers to the Da and rhombicity for alignment medium t

			First, obtain a good estimate of the magnitude of Da and R from alignment tensors using either [[REDCAT\|REDCAT]] or PALES program and use this as a starting point for the refinement. Then edit the following portion of the refine.py script. Note: text on the same line and following a “#” sign is not read by the XPLOR program.

			:'''('t', -6.5, 0.62)''': this line refers to the Da and rhombicity for alignment medium t
	<pre># medium Da rhombicity		<pre># medium Da rhombicity
	for (medium,Da,Rh) in [ ('t', -6.5, 0.62),		for (medium,Da,Rh) in [ ('t', -6.5, 0.62),
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	pass		pass
	potList.append(rdcs)		potList.append(rdcs)
	rampedParams.append( MultRamp(0.05,5.0, "rdcs.setScale( VALUE )") )		rampedParams.append( MultRamp(0.05,0.25, "rdcs.setScale( VALUE )") )
	</pre>		</pre>
	<br> Allow Da and R to float by using the setFreedom method associated with the medium object. To fix the peptide plane, the IVM_groupRigidBackbone tool were used (First two lines and the last line).		<br> Allow Da and R to float by using the setFreedom method associated with the medium object. To fix the peptide plane, the IVM_groupRigidBackbone tool were used (First two lines and the last line).

Hlee at 19:38, 22 March 2012

2012-03-22T19:38:46Z

← Older revision		Revision as of 19:38, 22 March 2012
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	RCSAs can also be used to validate protein structure using [[REDCAT\|REDCAT]].		RCSAs can also be used to validate protein structure using [[REDCAT\|REDCAT]].

			Unlike RDCs which are defined with a single vector, RCSAs require a full 3 axis system. This is usually defined by identifying a set of 3 bonded atoms.

	:'''(resid 2 and name C) (resid 3 and name N) (resid 3 and name HN) 29.040 24.750''': 29.040 is the N RCSA shift in PPB unit and 24.750 is a constant		:'''(resid 2 and name C) (resid 3 and name N) (resid 3 and name HN) 29.040 24.750''': 29.040 is the N RCSA shift in PPB unit and 24.750 is a constant
	:'''(resid 4 and name C) (resid 4 and name O) (resid 5 and name N) -24.400 13.333''': -24.400 is the C RCSA shift in PPB unit and 13.333 is a constant		:'''(resid 4 and name C) (resid 4 and name O) (resid 5 and name N) -24.400 13.333''': -24.400 is the C RCSA shift in PPB unit and 13.333 is a constant
	<pre> #For N RCSA		<pre> #For N RCSA
	assign (resid 500 and name OO ) (resid 500 and name Z) (resid 500 and name X ) (resid 500 and name Y )		assign (resid 500 and name OO )
	(resid 2 and name C) (resid 3 and name N) (resid 3 and name HN) 29.040 24.750		(resid 500 and name Z)
			(resid 500 and name X )
			(resid 500 and name Y )
			(resid 2 and name C)
			(resid 3 and name N)
			(resid 3 and name HN) 29.040 24.750
	assign (resid 500 and name OO ) (resid 500 and name Z) (resid 500 and name X ) (resid 500 and name Y )		assign (resid 500 and name OO ) (resid 500 and name Z) (resid 500 and name X ) (resid 500 and name Y )
	(resid 3 and name C) (resid 4 and name N) (resid 4 and name HN) 62.205 24.750		(resid 3 and name C) (resid 4 and name N) (resid 4 and name HN) 62.205 24.750

Hlee at 19:33, 22 March 2012

2012-03-22T19:33:07Z

← Older revision		Revision as of 19:33, 22 March 2012
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	An example of the RCSA table in XPLOR format is shown below:		An example of the RCSA table in XPLOR format is shown below:

	RCSAs can also be used to validate protein structure using [[REDCAT\|REDCAT]]~~. It is important to check measurement of the RCSA and apply reference correction if necessary~~.		RCSAs can also be used to validate protein structure using [[REDCAT\|REDCAT]].

	:'''(resid 2 and name C) (resid 3 and name N) (resid 3 and name HN) 29.040 24.750''': 29.040 is the N RCSA shift in PPB unit and 24.750 is a constant		:'''(resid 2 and name C) (resid 3 and name N) (resid 3 and name HN) 29.040 24.750''': 29.040 is the N RCSA shift in PPB unit and 24.750 is a constant

Hlee at 19:30, 22 March 2012

2012-03-22T19:30:57Z

← Older revision		Revision as of 19:30, 22 March 2012
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	</pre>		</pre>

	==== ~~Generate~~ RCSA Restraint Table ====		==== RCSA Restraint Table ====

	An example of the RCSA table in XPLOR format is shown below:		An example of the RCSA table in XPLOR format is shown below:

	~~RCSA~~ can also be used to validate protein structure using [[REDCAT\|REDCAT]] ~~or Prestegard in house script~~. It is important to check measurement of the RCSA and apply reference correction if necessary.		RCSAs can also be used to validate protein structure using [[REDCAT\|REDCAT]]. It is important to check measurement of the RCSA and apply reference correction if necessary.

	:'''(resid 2 and name C) (resid 3 and name N) (resid 3 and name HN) 29.040 24.750''': 29.040 is the N RCSA shift in PPB unit and 24.750 is a constant		:'''(resid 2 and name C) (resid 3 and name N) (resid 3 and name HN) 29.040 24.750''': 29.040 is the N RCSA shift in PPB unit and 24.750 is a constant

Hlee at 19:29, 22 March 2012

2012-03-22T19:29:02Z

← Older revision		Revision as of 19:29, 22 March 2012
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	An example of the RDC table in XPLOR format is shown below:		An example of the RDC table in XPLOR format is shown below:

	:'''( resid 500 and name OO )''': resid 500 is the residue number for the tensor		:'''( resid 500 and name OO )''': resid 500 is the residue number for the tensor axis system
	:'''( resid 3 and name N )''': ~~resid 3: residue number~~ of ~~each amino acid~~		:'''( resid # and name N )''': defines the first atom of the pair
	:'''( resid 3 and name HN ) 2.586 1.5''': RDC_value, Error_value		:'''( resid # and name HN ) 2.586 1.5''': defines the second atom of the pair, RDC_value, Error_value
	::'''Note''': The error_value is not ~~critical due to~~ the ~~minimization style~~ of this script.		::'''Note''': The error_value term is not utilized with the square potential of this script.
	<pre># For NH Coupling		<pre># For NH Coupling
	assign ( resid 500 and name OO )		assign ( resid 500 and name OO )