FOUND - Revision history

Jma at 21:48, 6 January 2010

2010-01-06T21:48:05Z

← Older revision		Revision as of 21:48, 6 January 2010
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	== '''Introduction''' ==		== '''Introduction''' ==

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	'''N.B.''' The <tt>GridSearch.cya</tt> script is not the same as the <tt>grid search</tt> command!		'''N.B.''' The <tt>GridSearch.cya</tt> script is not the same as the <tt>grid search</tt> command!

	<br>		<br>

	== '''Verifying Local NOE Network''' ==		== '''Verifying Local NOE Network''' ==
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	In subsequent steps it is recommended to swap the labels in the original source containing chemical shift assignments: the atom list if using XEASY, or CARA repository if using CARA.		In subsequent steps it is recommended to swap the labels in the original source containing chemical shift assignments: the atom list if using XEASY, or CARA repository if using CARA.
			<br>
	<br>~~-- GaohuaLiu - 26 Jan 2007~~

	~~-- Edited by JimAramini - Nov 2009~~

	<br>		<br>

Jma at 16:26, 13 November 2009

2009-11-13T16:26:34Z

← Older revision		Revision as of 16:26, 13 November 2009
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	#Create a working subdirectory (for example, <tt>structure/cyana21/found</tt>).		#Create a working subdirectory (for example, <tt>structure/cyana21/found</tt>).
	#If you have ct-[~~13C~~,1H]-HSQC spectra for the fractionally ~~13C~~-labeled sample, determine the stereospecific assignments for Val and Leu methyl groups and swap spin labels (in the XEASY atom list or CARA repository) where necessary, as described in [[NESG:SSAFromFractional13CLabeledSample\|Stereospecific assignments from fractionally 13C-labeled sample]]. Create a file <tt>stereo.cya</tt> to declare the residues, for which stereospecific assignments were established.		#If you have ct-[<sup>13</sup>C,<sup>1</sup>H]-HSQC spectra for the fractionally <sup>13</sup>C-labeled sample, determine the stereospecific assignments for Val and Leu methyl groups and swap spin labels (in the XEASY atom list or CARA repository) where necessary, as described in [[NESG:SSAFromFractional13CLabeledSample\|Stereospecific assignments from fractionally 13C-labeled sample]]. Create a file <tt>stereo.cya</tt> to declare the residues, for which stereospecific assignments were established.
	#Copy the latest sequence (<tt>XXXX.seq</tt>), atomlist (<tt>XXXX.prot</tt>) and peaklist files (<tt>n.peaks</tt>, <tt>ali.peaks</tt> and <tt>aro.peaks</tt>) into the working directory. Modify the sequence file if you have non-standard residues, such as cis-proline (use <tt>cPRO</tt>).		#Copy the latest sequence (<tt>XXXX.seq</tt>), atomlist (<tt>XXXX.prot</tt>) and peaklist files (<tt>n.peaks</tt>, <tt>ali.peaks</tt> and <tt>aro.peaks</tt>) into the working directory. Modify the sequence file if you have non-standard residues, such as cis-proline (use <tt>cPRO</tt>).
	#Create an init.cya file as described in "[[NESG:CYANAInitFile\|Creating an init.cya file for CYANA 2.1]]" or copy a previously used file. Set an appropriate RMSD calculation range.		#Create an init.cya file as described in "[[NESG:CYANAInitFile\|Creating an init.cya file for CYANA 2.1]]" or copy a previously used file. Set an appropriate RMSD calculation range.
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	'''N.B.''' The <tt>GridSearch.cya</tt> script is not the same as the <tt>grid search</tt> command!		'''N.B.''' The <tt>GridSearch.cya</tt> script is not the same as the <tt>grid search</tt> command!

	<br>		<br>

	== '''Verifying Local NOE Network''' ==		== '''Verifying Local NOE Network''' ==

Jma at 22:10, 5 November 2009

2009-11-05T22:10:54Z

← Older revision		Revision as of 22:10, 5 November 2009
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	~~= '''FOUND(HABAS)''' =~~

	== '''Introduction''' ==		== '''Introduction''' ==

Jma at 18:59, 4 November 2009

2009-11-04T18:59:10Z

← Older revision		Revision as of 18:59, 4 November 2009
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	#Copy the latest sequence (<tt>XXXX.seq</tt>), atomlist (<tt>XXXX.prot</tt>) and peaklist files (<tt>n.peaks</tt>, <tt>ali.peaks</tt> and <tt>aro.peaks</tt>) into the working directory. Modify the sequence file if you have non-standard residues, such as cis-proline (use <tt>cPRO</tt>).		#Copy the latest sequence (<tt>XXXX.seq</tt>), atomlist (<tt>XXXX.prot</tt>) and peaklist files (<tt>n.peaks</tt>, <tt>ali.peaks</tt> and <tt>aro.peaks</tt>) into the working directory. Modify the sequence file if you have non-standard residues, such as cis-proline (use <tt>cPRO</tt>).
	#Create an init.cya file as described in "[[NESG:CYANAInitFile\|Creating an init.cya file for CYANA 2.1]]" or copy a previously used file. Set an appropriate RMSD calculation range.		#Create an init.cya file as described in "[[NESG:CYANAInitFile\|Creating an init.cya file for CYANA 2.1]]" or copy a previously used file. Set an appropriate RMSD calculation range.
	#Create a <tt>GridSearch.cya</tt> file or download a template [[~~media~~:GridSearch.cya\|GridSearch.cya]] (see below).		#Create a <tt>GridSearch.cya</tt> file or download a template [[Media:GridSearch.cya\|GridSearch.cya]] (see below).
	#Copy the TALOS dihedral angel constraints file (<tt>talos.aco</tt>) from the previous step. Keep only those constraints, which correspond to residues in the secondary structure elements according to CSI, excluding one residue at the edge of each element. You can comment out the remaining lines with a hash character =#= using any text editor.		#Copy the TALOS dihedral angel constraints file (<tt>talos.aco</tt>) from the previous step. Keep only those constraints, which correspond to residues in the secondary structure elements according to CSI, excluding one residue at the edge of each element. You can comment out the remaining lines with a hash character =#= using any text editor.
	#Produce initial calibration as described in NOECalibrationCYANA#Finding_Initial_NOE_Calibration.		#Produce initial calibration as described in NOECalibrationCYANA#Finding_Initial_NOE_Calibration.
	#Download the [[~~media~~:~~CALC~~.cya\|CALC.cya]] file to run a test structure calculation using the output of FOUND (see below).		#Download the [[Media:CALC_found.cya\|CALC.cya]] file to run a test structure calculation using the output of FOUND (see below).

	Here is the template <tt>GridSearch.cya</tt> script adapted from <tt>~/demos/details/GridSearch.cya</tt> in CYANA 2.1 installation directory. The options for scalar couplings have been commented out since they aren't routinely used.		Here is the template <tt>GridSearch.cya</tt> script adapted from <tt>~/demos/details/GridSearch.cya</tt> in CYANA 2.1 installation directory. The options for scalar couplings have been commented out since they aren't routinely used.
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	<br>		<br>

	*[[~~media~~:GridSearch.cya\|GridSearch.cya]]: CYANA script to run FOUND module		*[[Media:GridSearch.cya\|GridSearch.cya]]: CYANA script to run FOUND module

	*[[~~media~~:~~CALC~~.cya\|CALC.cya]]: CYANA script to run manual calculation with local constraints		*[[Media:CALC_found.cya\|CALC.cya]]: CYANA script to run manual calculation with local constraints

Jma at 17:46, 4 November 2009

2009-11-04T17:46:12Z

Jma at 17:44, 4 November 2009

2009-11-04T17:44:16Z

← Older revision		Revision as of 17:44, 4 November 2009
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	In subsequent steps it is recommended to swap the labels in the original source containing chemical shift assignments: the atom list if using XEASY, or CARA repository if using CARA.		In subsequent steps it is recommended to swap the labels in the original source containing chemical shift assignments: the atom list if using XEASY, or CARA repository if using CARA.

	<br>-- ~~Main.~~GaohuaLiu - 26 Jan 2007		<br>-- GaohuaLiu - 26 Jan 2007

			-- Edited by JimAramini - Nov 2009

	<br>		<br>

Jma at 19:12, 3 November 2009

2009-11-03T19:12:57Z

← Older revision		Revision as of 19:12, 3 November 2009
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	References:<br> FOUND - [http://www.springerlink.com/content/t318k12296032kk5/fulltext.pdf Guntert P. ''J. Biomol. NMR'' 12 (4): 543-548 NOV 1998]<br> HABAS - [http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1989/111/i11/pdf/ja00193a036.pdf Guntert P. ''J. Am. Chem. Soc.'' 1989, 111, 3997-4004]		References:<br> FOUND - [http://www.springerlink.com/content/t318k12296032kk5/fulltext.pdf Guntert P. ''J. Biomol. NMR'' 12 (4): 543-548 NOV 1998]<br> HABAS - [http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1989/111/i11/pdf/ja00193a036.pdf Guntert P. ''J. Am. Chem. Soc.'' 1989, 111, 3997-4004]

			<br>

			== '''How FOUND (HABAS) Works'''<br> ==

			[[Image:Found3.jpg]]<br>

	~~== '''How FOUND (HABAS) Works'''<br> ==~~

	~~[[Image:Found3.jpg]]~~
	==

	== '''Preparing to run FOUND (HABAS)''' ==		== '''Preparing to run FOUND (HABAS)''' ==
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	'''N.B.''' The <tt>GridSearch.cya</tt> script is not the same as the <tt>grid search</tt> command!		'''N.B.''' The <tt>GridSearch.cya</tt> script is not the same as the <tt>grid search</tt> command!

			<br>

	== '''Verifying Local NOE Network''' ==		== '''Verifying Local NOE Network''' ==
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	*<tt>gridsearch.aco</tt> - is a combination of input TALOS constraints and constraints generated with the grid search method.		*<tt>gridsearch.aco</tt> - is a combination of input TALOS constraints and constraints generated with the grid search method.

			<br>

	== '''Stereospecific Assignments from FOUND (HABAS)''' ==		== '''Stereospecific Assignments from FOUND (HABAS)''' ==

Jma at 19:12, 3 November 2009

2009-11-03T19:12:18Z

← Older revision		Revision as of 19:12, 3 November 2009
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	References:<br> FOUND - [http://www.springerlink.com/content/t318k12296032kk5/fulltext.pdf Guntert P. ''J. Biomol. NMR'' 12 (4): 543-548 NOV 1998]<br> HABAS - [http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1989/111/i11/pdf/ja00193a036.pdf Guntert P. ''J. Am. Chem. Soc.'' 1989, 111, 3997-4004]		References:<br> FOUND - [http://www.springerlink.com/content/t318k12296032kk5/fulltext.pdf Guntert P. ''J. Biomol. NMR'' 12 (4): 543-548 NOV 1998]<br> HABAS - [http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1989/111/i11/pdf/ja00193a036.pdf Guntert P. ''J. Am. Chem. Soc.'' 1989, 111, 3997-4004]



	== '''How FOUND (HABAS) Works'''<br> ==		== '''How FOUND (HABAS) Works'''<br> ==

	[[Image:Found3.jpg]]		[[Image:Found3.jpg]]
			==

	== '''Preparing to run FOUND (HABAS)''' ==		== '''Preparing to run FOUND (HABAS)''' ==
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	'''N.B.''' The <tt>GridSearch.cya</tt> script is not the same as the <tt>grid search</tt> command!		'''N.B.''' The <tt>GridSearch.cya</tt> script is not the same as the <tt>grid search</tt> command!



	== '''Verifying Local NOE Network''' ==		== '''Verifying Local NOE Network''' ==
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	*<tt>swapped.upl</tt> - a modification of the input UPL file, in which spin labels have been swapped according to the newly derived stereospecific assignments. This file itself is not used in subsequent automated structure calculation and NOE assignment, because of incompatible NOE calibration protocols.		*<tt>swapped.upl</tt> - a modification of the input UPL file, in which spin labels have been swapped according to the newly derived stereospecific assignments. This file itself is not used in subsequent automated structure calculation and NOE assignment, because of incompatible NOE calibration protocols.
	*<tt>gridsearch.aco</tt> - is a combination of input TALOS constraints and constraints generated with the grid search method.		*<tt>gridsearch.aco</tt> - is a combination of input TALOS constraints and constraints generated with the grid search method.



	== '''Stereospecific Assignments from FOUND (HABAS)''' ==		== '''Stereospecific Assignments from FOUND (HABAS)''' ==

Jma at 19:10, 3 November 2009

2009-11-03T19:10:08Z

← Older revision		Revision as of 19:10, 3 November 2009
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	== '''FOUND(HABAS)''' ==		= '''FOUND(HABAS)''' =

			== '''Introduction''' ==
	=== '''Introduction''' ===

	'''FOUND''' performs systematic local conformation analysis by exhaustive grid searches for arbitrary contiguous fragments of proteins and nucleic acids. It uses torsion angles as the only degrees of freedom to identify all conformations that fulfill the steric and NMR-derived conformational restraints within a contiguous molecular fragment, as defined either by limits on the maximal restraint violations or by the fragment-based target function value.		'''FOUND''' performs systematic local conformation analysis by exhaustive grid searches for arbitrary contiguous fragments of proteins and nucleic acids. It uses torsion angles as the only degrees of freedom to identify all conformations that fulfill the steric and NMR-derived conformational restraints within a contiguous molecular fragment, as defined either by limits on the maximal restraint violations or by the fragment-based target function value.
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	angles=side-chain angles (default: CHI1)		angles=side-chain angles (default: CHI1)
	tfcut=fmax (default: 0.0)		tfcut=fmax (default: 0.0)
	continue</pre>		continue</pre>
	<br> Performs for all amino acid residues in the given range grid searches comprising the backbone dihedral angles φ, ψ, χ1 and the given side-chain angles. To specify more than one side-chain angle, the names must be given, separated by blanks and enclosed in double quotes. If the cutoff value for the local, fragment-based target function, <tt>fmax</tt>, is positive, then all conformations with a local target function value below <tt>fmax</tt> will be considered as allowed. Otherwise, a conformation will be allowed if no single restraint violation exceeds the corresponding cutoff value defined by the variables <tt>soft_upl</tt>, <tt>soft_lol</tt>, etc. Unless the <tt>continue</tt> option is set, the allowed ranges of dihedral angles will be initialized to allow all possible angle values before the grid searches are started.		<br> Performs for all amino acid residues in the given range grid searches comprising the backbone dihedral angles φ, ψ, χ1 and the given side-chain angles. To specify more than one side-chain angle, the names must be given, separated by blanks and enclosed in double quotes. If the cutoff value for the local, fragment-based target function, <tt>fmax</tt>, is positive, then all conformations with a local target function value below <tt>fmax</tt> will be considered as allowed. Otherwise, a conformation will be allowed if no single restraint violation exceeds the corresponding cutoff value defined by the variables <tt>soft_upl</tt>, <tt>soft_lol</tt>, etc. Unless the <tt>continue</tt> option is set, the allowed ranges of dihedral angles will be initialized to allow all possible angle values before the grid searches are started.

	FOUND is implemented as a CYANA and DYANA macro succeeding the standalone HABAS program. Therefore, the FOUND macros are called <tt>habas.cya</tt> or <tt>habas.dya</tt>. For more information type <tt>help habas</tt> in CYANA or see the reference below.		FOUND is implemented as a CYANA and DYANA macro succeeding the standalone HABAS program. Therefore, the FOUND macros are called <tt>habas.cya</tt> or <tt>habas.dya</tt>. For more information type <tt>help habas</tt> in CYANA or see the reference below.

	References:<br> FOUND - [http://www.springerlink.com/content/t318k12296032kk5/fulltext.pdf Guntert P. ''J. Biomol. NMR'' 12 (4): 543-548 NOV 1998]<br> HABAS - [http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1989/111/i11/pdf/ja00193a036.pdf Guntert P. ''J. Am. Chem. Soc.'' 1989, 111, 3997-4004]		References:<br> FOUND - [http://www.springerlink.com/content/t318k12296032kk5/fulltext.pdf Guntert P. ''J. Biomol. NMR'' 12 (4): 543-548 NOV 1998]<br> HABAS - [http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1989/111/i11/pdf/ja00193a036.pdf Guntert P. ''J. Am. Chem. Soc.'' 1989, 111, 3997-4004]

	=== '''How FOUND (HABAS) Works'''<br> ===		== '''How FOUND (HABAS) Works'''<br> ==

	[[Image:Found3.jpg]]		[[Image:Found3.jpg]]

	=== '''Preparing to run FOUND (HABAS)''' ===		== '''Preparing to run FOUND (HABAS)''' ==

	If you are using completely unassigned peaklists and you don't have any J-coupling data, then you don't need to run found. Otherwise, do the following:		If you are using completely unassigned peaklists and you don't have any J-coupling data, then you don't need to run found. Otherwise, do the following:
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	savestereo stereofound.cya # write macro with stereospecific assignments		savestereo stereofound.cya # write macro with stereospecific assignments
	protocol:=		protocol:=
	</pre>		</pre>
			<br> It is recommended to apply [[NESG:SSAFromFractional13CLabeledSample\|stereospecific assignments of Leu and Val isopropyl groups]] (if available) when running HABAS. This may help HABAS derive additional stereospecific assignments for HB2/3 spins of Leu. To take advantage of stereospecific assignments create <tt>swap.cya</tt> and <tt>stereo.cya</tt> macros as described in the topic about [[NESG:ApplyingSSA\|applying stereospecific assignments]] and use them to generate a swapped proton list and a swapped UPL file <tt>short.upl</tt>

			'''N.B.''' The <tt>GridSearch.cya</tt> script is not the same as the <tt>grid search</tt> command!

			== '''Verifying Local NOE Network''' ==

	~~It is recommended to apply [[NESG:SSAFromFractional13CLabeledSample\|stereospecific assignments of Leu and Val isopropyl groups]] (if available) when running HABAS~~. ~~This may help HABAS derive additional stereospecific assignments for HB2/3 spins of Leu. To take advantage of stereospecific assignments create~~ <tt>~~swap~~.cya</tt> ~~and~~ <tt>~~stereo~~.cya</tt> ~~macros as described~~ in the ~~topic about [[NESG:ApplyingSSA\|applying stereospecific assignments]] and use them to generate a swapped proton list and a swapped UPL file~~ <tt>~~short~~.~~upl~~</tt>		#In CYANA 2.1 run the <tt>GridSearch.cya</tt> script.
			#In CYANA 2.1 run the <tt>CALC.cya</tt> script. This may take several minutes on a workstation.
			#Go residue-by-residue through the FOUND output. If inconsistent data was found, double-check the NOE peaks for this residue in XEASY or CARA. UPL violations reported in the <tt>XXXX.ovw</tt> file usually help to pinpoint the questionable peaks.

	'''N.B.''' ~~The <tt>GridSearch~~.~~cya</tt> script is not~~ the ~~same as~~ the <tt>~~grid search~~</tt> ~~command!~~		**Usually ''inconsistent data'' reports are caused by peaks with improper volumes or incorrectly assigned peaks. Check assignments and integration in XEASY or CARA.
			**Too many ''inconsistent data'' reports and violations for apparently valid peaks indicate that calibration that is too tight. Look at the violations in the <tt>XXXX.ovw</tt> file to determine which peaklist requires calibration adjustment. Change calibration constants and re-run the calibration.

	~~=== '''Verifying Local NOE Network''' ===~~		#Repeat steps 1 and 3 until no inconsistent data was found by FOUND and the average target function is < 0.5 .

	~~# In CYANA 2.1 run the <tt>GridSearch.cya</tt> script.~~		FOUND will produce the following files:
	~~# In CYANA 2.1 run the <tt>CALC.cya</tt> script. This may take several minutes on a workstation.~~
	# Go residue-by-residue through the FOUND output. If inconsistent data was found, double-check the NOE peaks for this residue in XEASY or CARA. UPL violations reported in the <tt>XXXX.ovw</tt> file usually help to pinpoint the questionable peaks.
	** Usually ''inconsistent data'' reports are caused by peaks with improper volumes or incorrectly assigned peaks. Check assignments and integration in XEASY or CARA.
	** Too many ''inconsistent data'' reports and violations for apparently valid peaks indicate that calibration that is too tight. Look at the violations in the <tt>XXXX.ovw</tt> file to determine which peaklist requires calibration adjustment. Change calibration constants and re-run the calibration.
	~~# Repeat steps 1 and 3 until no inconsistent data was found by~~ FOUND ~~and~~ the ~~average target function is < 0.5 .~~

	~~FOUND will produce the following files:~~		*<tt>stereofound.cya</tt> - CYANA script, which delcares stereospecific assignments. It is a combination of input stereospecific assignments and those generated by FOUND.
	* <tt>stereofound.cya</tt> - CYANA script, which delcares stereospecific assignments. It is a combination of input stereospecific assignments and those generated by FOUND.		*<tt>swapped.upl</tt> - a modification of the input UPL file, in which spin labels have been swapped according to the newly derived stereospecific assignments. This file itself is not used in subsequent automated structure calculation and NOE assignment, because of incompatible NOE calibration protocols.
	* <tt>swapped.upl</tt> - a modification of the input UPL file, in which spin labels have been swapped according to the newly derived stereospecific assignments. This file itself is not used in subsequent automated structure calculation and NOE assignment, because of incompatible NOE calibration protocols.		*<tt>gridsearch.aco</tt> - is a combination of input TALOS constraints and constraints generated with the grid search method.
	* <tt>gridsearch.aco</tt> - is a combination of input TALOS constraints and constraints generated with the grid search method.

	=== '''Stereospecific Assignments from FOUND (HABAS)''' ===		== '''Stereospecific Assignments from FOUND (HABAS)''' ==

	Stereo-specific assignment can be obtain from checking FOUND module without any preliminary structure. FOUND module performing separate grid searches for both possible stereospecific assignments for diastereotopic protons or isopropyl groups as show in the figure below:<br>		Stereo-specific assignment can be obtain from checking FOUND module without any preliminary structure. FOUND module performing separate grid searches for both possible stereospecific assignments for diastereotopic protons or isopropyl groups as show in the figure below:<br>

	[[Image:Found6.jpg]]		[[Image:Found6.jpg]]

	where the allowed conformation numbers for the two possible stereospecific assignments are N1 and N2, separately		where the allowed conformation numbers for the two possible stereospecific assignments are N1 and N2, separately
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	45 MET HB2 HB3 assigned		45 MET HB2 HB3 assigned
	45 MET HG2 HG3		45 MET HG2 HG3
	</pre>		</pre>
	See the data upstream from the summary to find whether atom pair were assigned "swapped" or "as input". Verify that peaks assigned to the reported spins are integrated correctly. Avoid accepting assignments with very few allowed conformations (such as Met45 below), because they are indicative of too tight UPLs.		See the data upstream from the summary to find whether atom pair were assigned "swapped" or "as input". Verify that peaks assigned to the reported spins are integrated correctly. Avoid accepting assignments with very few allowed conformations (such as Met45 below), because they are indicative of too tight UPLs.
	<pre> ARG 33:		<pre> ARG 33:
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	HB2/HB3 MET 45: 35/0 conformations, assigned as input.		HB2/HB3 MET 45: 35/0 conformations, assigned as input.
	HG2/HG3 MET 45: 14/21 conformations, unassigned.		HG2/HG3 MET 45: 14/21 conformations, unassigned.
	</pre>		</pre>
	Delete or comment out those lines in <tt>stereofound.cya</tt>, which you think correspond to incorrectly derived stereospecific assignments.		Delete or comment out those lines in <tt>stereofound.cya</tt>, which you think correspond to incorrectly derived stereospecific assignments.

Jma at 17:56, 31 October 2009

2009-10-31T17:56:05Z

← Older revision		Revision as of 17:46, 4 November 2009
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	== '''How FOUND (HABAS) Works'''<br> ==		== '''How FOUND (HABAS) Works'''<br> ==

	[[Image:Found3.jpg]]<br>		[[Image:Found3.jpg]]<br>


			<br>

	== '''Preparing to run FOUND (HABAS)''' ==		== '''Preparing to run FOUND (HABAS)''' ==
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	#Copy the latest sequence (<tt>XXXX.seq</tt>), atomlist (<tt>XXXX.prot</tt>) and peaklist files (<tt>n.peaks</tt>, <tt>ali.peaks</tt> and <tt>aro.peaks</tt>) into the working directory. Modify the sequence file if you have non-standard residues, such as cis-proline (use <tt>cPRO</tt>).		#Copy the latest sequence (<tt>XXXX.seq</tt>), atomlist (<tt>XXXX.prot</tt>) and peaklist files (<tt>n.peaks</tt>, <tt>ali.peaks</tt> and <tt>aro.peaks</tt>) into the working directory. Modify the sequence file if you have non-standard residues, such as cis-proline (use <tt>cPRO</tt>).
	#Create an init.cya file as described in "[[NESG:CYANAInitFile\|Creating an init.cya file for CYANA 2.1]]" or copy a previously used file. Set an appropriate RMSD calculation range.		#Create an init.cya file as described in "[[NESG:CYANAInitFile\|Creating an init.cya file for CYANA 2.1]]" or copy a previously used file. Set an appropriate RMSD calculation range.
	#Create a <tt>GridSearch.cya</tt> file or download a template [[~~NESG~~:~~%ATTACHURL%/~~GridSearch.cya\|GridSearch.cya]] (see below).		#Create a <tt>GridSearch.cya</tt> file or download a template [[media:GridSearch.cya\|GridSearch.cya]] (see below).
	#Copy the TALOS dihedral angel constraints file (<tt>talos.aco</tt>) from the previous step. Keep only those constraints, which correspond to residues in the secondary structure elements according to CSI, excluding one residue at the edge of each element. You can comment out the remaining lines with a hash character =#= using any text editor.		#Copy the TALOS dihedral angel constraints file (<tt>talos.aco</tt>) from the previous step. Keep only those constraints, which correspond to residues in the secondary structure elements according to CSI, excluding one residue at the edge of each element. You can comment out the remaining lines with a hash character =#= using any text editor.
	#Produce initial calibration as described in NOECalibrationCYANA#Finding_Initial_NOE_Calibration.		#Produce initial calibration as described in NOECalibrationCYANA#Finding_Initial_NOE_Calibration.
	#Download the [[~~NESG~~:~~%ATTACHURL%/~~CALC.cya\|CALC.cya]] file to run a test structure calculation using the output of FOUND (see below).		#Download the [[media:CALC.cya\|CALC.cya]] file to run a test structure calculation using the output of FOUND (see below).

	Here is the template <tt>GridSearch.cya</tt> script adapted from <tt>~/demos/details/GridSearch.cya</tt> in CYANA 2.1 installation directory. The options for scalar couplings have been commented out since they aren't routinely used.		Here is the template <tt>GridSearch.cya</tt> script adapted from <tt>~/demos/details/GridSearch.cya</tt> in CYANA 2.1 installation directory. The options for scalar couplings have been commented out since they aren't routinely used.
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	<br>-- GaohuaLiu - 26 Jan 2007		<br>-- GaohuaLiu - 26 Jan 2007

	-- Edited by JimAramini - Nov 2009		-- Edited by JimAramini - Nov 2009

	<br>		<br>

	*[[~~NESG~~:~~%ATTACHURL%/~~GridSearch.cya\|GridSearch.cya]]: CYANA script to run FOUND module		*[[media:GridSearch.cya\|GridSearch.cya]]: CYANA script to run FOUND module

	*[[~~NESG~~:~~%ATTACHURL%/~~CALC.cya\|CALC.cya]]: CYANA script to run manual calculation with local constraints		*[[media:CALC.cya\|CALC.cya]]: CYANA script to run manual calculation with local constraints

← Older revision		Revision as of 17:56, 31 October 2009
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	[[Image:Found3.jpg]]		[[Image:Found3.jpg]]

	=== '''Preparing to run FOUND (HABAS)''' ===		=== '''Preparing to run FOUND (HABAS)''' ===

	If you are using completely unassigned peaklists and you don't have any J-coupling data, then you don't need to run found. Otherwise, do the following:		If you are using completely unassigned peaklists and you don't have any J-coupling data, then you don't need to run found. Otherwise, do the following:

	# Create a working subdirectory (for example, <tt>structure/cyana21/found</tt>).		#Create a working subdirectory (for example, <tt>structure/cyana21/found</tt>).
	# If you have ct-[13C,1H]-HSQC spectra for the fractionally 13C-labeled sample, determine the stereospecific assignments for Val and Leu methyl groups and swap spin labels (in the XEASY atom list or CARA repository) where necessary, as described in [[NESG:SSAFromFractional13CLabeledSample\|Stereospecific assignments from fractionally 13C-labeled sample]]. Create a file <tt>stereo.cya</tt> to declare the residues, for which stereospecific assignments were established.		#If you have ct-[13C,1H]-HSQC spectra for the fractionally 13C-labeled sample, determine the stereospecific assignments for Val and Leu methyl groups and swap spin labels (in the XEASY atom list or CARA repository) where necessary, as described in [[NESG:SSAFromFractional13CLabeledSample\|Stereospecific assignments from fractionally 13C-labeled sample]]. Create a file <tt>stereo.cya</tt> to declare the residues, for which stereospecific assignments were established.
	# Copy the latest sequence (<tt>XXXX.seq</tt>), atomlist (<tt>XXXX.prot</tt>) and peaklist files (<tt>n.peaks</tt>, <tt>ali.peaks</tt> and <tt>aro.peaks</tt>) into the working directory. Modify the sequence file if you have non-standard residues, such as cis-proline (use <tt>cPRO</tt>).		#Copy the latest sequence (<tt>XXXX.seq</tt>), atomlist (<tt>XXXX.prot</tt>) and peaklist files (<tt>n.peaks</tt>, <tt>ali.peaks</tt> and <tt>aro.peaks</tt>) into the working directory. Modify the sequence file if you have non-standard residues, such as cis-proline (use <tt>cPRO</tt>).
	# Create an init.cya file as described in "[[NESG:CYANAInitFile\|Creating an init.cya file for CYANA 2.1]]" or copy a previously used file. Set an appropriate RMSD calculation range.		#Create an init.cya file as described in "[[NESG:CYANAInitFile\|Creating an init.cya file for CYANA 2.1]]" or copy a previously used file. Set an appropriate RMSD calculation range.
	# Create a <tt>GridSearch.cya</tt> file or download a template [[NESG:%ATTACHURL%/GridSearch.cya\|GridSearch.cya]] (see below).		#Create a <tt>GridSearch.cya</tt> file or download a template [[NESG:%ATTACHURL%/GridSearch.cya\|GridSearch.cya]] (see below).
	# Copy the TALOS dihedral angel constraints file (<tt>talos.aco</tt>) from the previous step. Keep only those constraints, which correspond to residues in the secondary structure elements according to CSI, excluding one residue at the edge of each element. You can comment out the remaining lines with a hash character =#= using any text editor.		#Copy the TALOS dihedral angel constraints file (<tt>talos.aco</tt>) from the previous step. Keep only those constraints, which correspond to residues in the secondary structure elements according to CSI, excluding one residue at the edge of each element. You can comment out the remaining lines with a hash character =#= using any text editor.
	# Produce initial calibration as described in NOECalibrationCYANA#Finding_Initial_NOE_Calibration.		#Produce initial calibration as described in NOECalibrationCYANA#Finding_Initial_NOE_Calibration.
	# Download the [[NESG:%ATTACHURL%/CALC.cya\|CALC.cya]] file to run a test structure calculation using the output of FOUND (see below).		#Download the [[NESG:%ATTACHURL%/CALC.cya\|CALC.cya]] file to run a test structure calculation using the output of FOUND (see below).

	Here is the template <tt>GridSearch.cya</tt> script adapted from <tt>~/demos/details/GridSearch.cya</tt> in CYANA 2.1 installation directory. The options for scalar couplings have been commented out since they aren't routinely used.		Here is the template <tt>GridSearch.cya</tt> script adapted from <tt>~/demos/details/GridSearch.cya</tt> in CYANA 2.1 installation directory. The options for scalar couplings have been commented out since they aren't routinely used.
			<pre>protocol:=found.out
	<~~nowiki~~>
	protocol:=found.out
	read seq $name.seq		read seq $name.seq
	read upl short.upl # read noe upper distance limits		read upl short.upl # read noe upper distance limits
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	savestereo stereofound.cya # write macro with stereospecific assignments		savestereo stereofound.cya # write macro with stereospecific assignments
	protocol:=		protocol:=
	</~~nowiki~~>		</pre>


	It is recommended to apply [[NESG:SSAFromFractional13CLabeledSample\|stereospecific assignments of Leu and Val isopropyl groups]] (if available) when running HABAS. This may help HABAS derive additional stereospecific assignments for HB2/3 spins of Leu. To take advantage of stereospecific assignments create <tt>swap.cya</tt> and <tt>stereo.cya</tt> macros as described in the topic about [[NESG:ApplyingSSA\|applying stereospecific assignments]] and use them to generate a swapped proton list and a swapped UPL file <tt>short.upl</tt>		It is recommended to apply [[NESG:SSAFromFractional13CLabeledSample\|stereospecific assignments of Leu and Val isopropyl groups]] (if available) when running HABAS. This may help HABAS derive additional stereospecific assignments for HB2/3 spins of Leu. To take advantage of stereospecific assignments create <tt>swap.cya</tt> and <tt>stereo.cya</tt> macros as described in the topic about [[NESG:ApplyingSSA\|applying stereospecific assignments]] and use them to generate a swapped proton list and a swapped UPL file <tt>short.upl</tt>

	'''N.B.''' The <tt>GridSearch.cya</tt> script is not the same as the <tt>grid search</tt> command!		'''N.B.''' The <tt>GridSearch.cya</tt> script is not the same as the <tt>grid search</tt> command!