LACS - Revision history

Jma at 16:56, 5 January 2010

2010-01-05T16:56:45Z

← Older revision		Revision as of 16:56, 5 January 2010
Line 100:		Line 100:
	<br>		<br>

	<br>		<br>

	~~-- PaoloRossi - 20 Nov 2009~~

Prossi at 21:35, 23 November 2009

2009-11-23T21:35:03Z

← Older revision		Revision as of 21:35, 23 November 2009
Line 96:		Line 96:
	In the NESG the IUPAC referencing is obtained using internal 50 uM DSS and setting the DSS methyl peak to 0.00 ppm at the temperature of interest.  The spectrometer temperature is calibrated using a neat methanol sample in the 10 - 40 °C range.  Under these conditions, backbone CS of double labeled protein samples derived from triple resonance experiments alone typically show small deviations 0.1 - 0.3 ppm in <sup>13</sup>C and 0.01 - 0.03 ppm in <sup>1</sup>H.  The final CS set derived from double labeled samples filtered through higher resolution [<sup>1</sup>H,<sup>13</sup>C]-HSQC tends to give offsets at the lower extreme of this range.  On a smaller statistical sampling of triply labeled proteins we found higher offset values (0.4 - 0.8 ppm) in CA and CB.  Offsett correction prior to TALOS or MFR runs are therefore highly recommended especially for the treatment of triply labeled samples.  <br>		In the NESG the IUPAC referencing is obtained using internal 50 uM DSS and setting the DSS methyl peak to 0.00 ppm at the temperature of interest.  The spectrometer temperature is calibrated using a neat methanol sample in the 10 - 40 °C range.  Under these conditions, backbone CS of double labeled protein samples derived from triple resonance experiments alone typically show small deviations 0.1 - 0.3 ppm in <sup>13</sup>C and 0.01 - 0.03 ppm in <sup>1</sup>H.  The final CS set derived from double labeled samples filtered through higher resolution [<sup>1</sup>H,<sup>13</sup>C]-HSQC tends to give offsets at the lower extreme of this range.  On a smaller statistical sampling of triply labeled proteins we found higher offset values (0.4 - 0.8 ppm) in CA and CB.  Offsett correction prior to TALOS or MFR runs are therefore highly recommended especially for the treatment of triply labeled samples.  <br>

			<br>

			<br>

			<br>



	-- PaoloRossi - 20 Nov 2009		-- PaoloRossi - 20 Nov 2009

Prossi at 21:22, 23 November 2009

2009-11-23T21:22:32Z

← Older revision		Revision as of 21:22, 23 November 2009
Line 94:		Line 94:
	== '''Practical Experience with Running LACS in the NESG''' ==		== '''Practical Experience with Running LACS in the NESG''' ==

	In the NESG the IUPAC referencing is obtained using internal 50 uM DSS and setting the DSS methyl peak to 0.00 ppm at the temperature of interest.  The spectrometer temperature is calibrated using a neat methanol sample in the 10 - 40 °C range.  Under these conditions, backbone CS of double labeled protein samples derived from triple resonance experiments alone typically show small deviations 0.1 - 0.3 ppm in <sup>13</sup>C and 0.01 - 0.03 ppm in <sup>1</sup>H.  The final CS set derived from double labeled samples filtered through higher resolution [<sup>1</sup>H,<sup>13</sup>C]-HSQC tends to give offsets at the lower extreme of this range.  On a smaller statistical sampling of triply labeled proteins we found higher offset values (0.4 - 0.8 ppm) in CA and CB.  Offsett correction prior to TALOS or MFR runs are therefore highly recommended especially for the treatment of triply labeled samples.		In the NESG the IUPAC referencing is obtained using internal 50 uM DSS and setting the DSS methyl peak to 0.00 ppm at the temperature of interest.  The spectrometer temperature is calibrated using a neat methanol sample in the 10 - 40 °C range.  Under these conditions, backbone CS of double labeled protein samples derived from triple resonance experiments alone typically show small deviations 0.1 - 0.3 ppm in <sup>13</sup>C and 0.01 - 0.03 ppm in <sup>1</sup>H.  The final CS set derived from double labeled samples filtered through higher resolution [<sup>1</sup>H,<sup>13</sup>C]-HSQC tends to give offsets at the lower extreme of this range.  On a smaller statistical sampling of triply labeled proteins we found higher offset values (0.4 - 0.8 ppm) in CA and CB.  Offsett correction prior to TALOS or MFR runs are therefore highly recommended especially for the treatment of triply labeled samples.  <br>


	~~ <br>~~

	~~<br>~~

	~~editing of this entry is in progress (prossi)<br>~~

	~~<br>~~

	~~<br>~~

	-- PaoloRossi - 20 Nov 2009		-- PaoloRossi - 20 Nov 2009

Prossi at 20:55, 23 November 2009

2009-11-23T20:55:02Z

← Older revision		Revision as of 20:55, 23 November 2009
Line 1:		Line 1:
	== '''Introduction''' ==		== '''Introduction''' ==

	Linear analysis of chemical shift ([http://www.ncbi.nlm.nih.gov/pubmed/16041479 LACS]) provides an independent means for absolute [[~~media~~:~~iupac~~.pdf\|referencing]] of protein chemical shifts.  LACS is routinely run on all chemical shift sets submitted to the BioMagResBank (BMRB).		Linear analysis of chemical shift ([http://www.ncbi.nlm.nih.gov/pubmed/16041479 LACS]) provides an independent means for absolute [[Media:Iupac.pdf\|referencing]] of protein chemical shifts.  LACS is routinely run on all chemical shift sets submitted to the BioMagResBank (BMRB).

	In the contest of protein structure determination chemical shifts (CS) play a key role as reporters of secondary structure.  Backbone chemical shift derived dihedral angles can be obtained through programs such as [http://www.ncbi.nlm.nih.gov/pubmed/19548092 TALOS+] and are used as constraints in the structure determination process. The backbone shift set (CA, CB, CO, HN, N, HA) is also used in the molecular fragment selection (MFR) for [http://www.ncbi.nlm.nih.gov/pubmed/18326625 CS-Rosetta] structure prediction protocol.  Here fragments are selected from the protein databank (PDB) that have the same predicted CS as the query sequence.  Successful use of chemical shift for secondary structure inference requires the correct referencing.  The LACS server gives independent CS offsets for CA, CB, CO and HA and allows for effective correction of chemical shift sets derived from [''U''-<sup>13</sup>C,<sup>15</sup>N] and from [''U''-<sup>2</sup>H,<sup>13</sup>C,<sup>15</sup>N].  The latter labeling scheme may show distinct degrees of offset for CA and CB due to the different number of bound deuterons which affect the value of the carbon to different degree.		In the contest of protein structure determination chemical shifts (CS) play a key role as reporters of secondary structure.  Backbone chemical shift derived dihedral angles can be obtained through programs such as [http://www.ncbi.nlm.nih.gov/pubmed/19548092 TALOS+] and are used as constraints in the structure determination process. The backbone shift set (CA, CB, CO, HN, N, HA) is also used in the molecular fragment selection (MFR) for [http://www.ncbi.nlm.nih.gov/pubmed/18326625 CS-Rosetta] structure prediction protocol.  Here fragments are selected from the protein databank (PDB) that have the same predicted CS as the query sequence.  Successful use of chemical shift for secondary structure inference requires the correct referencing.  The LACS server gives independent CS offsets for CA, CB, CO and HA and allows for effective correction of chemical shift sets derived from [''U''-<sup>13</sup>C,<sup>15</sup>N] and from [''U''-<sup>2</sup>H,<sup>13</sup>C,<sup>15</sup>N].  The latter labeling scheme may show distinct degrees of offset for CA and CB due to the different number of bound deuterons which affect the value of the carbon to different degree.

Prossi at 19:22, 20 November 2009

2009-11-20T19:22:24Z

← Older revision		Revision as of 19:22, 20 November 2009
Line 1:		Line 1:
	== '''Introduction''' ==		== '''Introduction''' ==

	Linear analysis of chemical shift ([http://www.ncbi.nlm.nih.gov/pubmed/16041479 LACS]) provides an independent means for absolute [[~~www.bmrb.wisc.edu/~~iupac.pdf\|referencing]] of protein chemical shifts.  LACS is routinely run on all chemical shift sets submitted to the BioMagResBank (BMRB).		Linear analysis of chemical shift ([http://www.ncbi.nlm.nih.gov/pubmed/16041479 LACS]) provides an independent means for absolute [[media:iupac.pdf\|referencing]] of protein chemical shifts.  LACS is routinely run on all chemical shift sets submitted to the BioMagResBank (BMRB).

	In the contest of protein structure determination chemical shifts (CS) play a key role as reporters of secondary structure.  Backbone chemical shift derived dihedral angles can be obtained through programs such as [http://www.ncbi.nlm.nih.gov/pubmed/19548092 TALOS+] and are used as constraints in the structure determination process. The backbone shift set (CA, CB, CO, HN, N, HA) is also used in the molecular fragment selection (MFR) for [http://www.ncbi.nlm.nih.gov/pubmed/18326625 CS-Rosetta] structure prediction protocol.  Here fragments are selected from the protein databank (PDB) that have the same predicted CS as the query sequence.  Successful use of chemical shift for secondary structure inference requires the correct referencing.  The LACS server gives independent CS offsets for CA, CB, CO and HA and allows for effective correction of chemical shift sets derived from [''U''-<sup>13</sup>C,<sup>15</sup>N] and from [''U''-<sup>2</sup>H,<sup>13</sup>C,<sup>15</sup>N].  The latter labeling scheme may show distinct degrees of offset for CA and CB due to the different number of bound deuterons which affect the value of the carbon to different degree.		In the contest of protein structure determination chemical shifts (CS) play a key role as reporters of secondary structure.  Backbone chemical shift derived dihedral angles can be obtained through programs such as [http://www.ncbi.nlm.nih.gov/pubmed/19548092 TALOS+] and are used as constraints in the structure determination process. The backbone shift set (CA, CB, CO, HN, N, HA) is also used in the molecular fragment selection (MFR) for [http://www.ncbi.nlm.nih.gov/pubmed/18326625 CS-Rosetta] structure prediction protocol.  Here fragments are selected from the protein databank (PDB) that have the same predicted CS as the query sequence.  Successful use of chemical shift for secondary structure inference requires the correct referencing.  The LACS server gives independent CS offsets for CA, CB, CO and HA and allows for effective correction of chemical shift sets derived from [''U''-<sup>13</sup>C,<sup>15</sup>N] and from [''U''-<sup>2</sup>H,<sup>13</sup>C,<sup>15</sup>N].  The latter labeling scheme may show distinct degrees of offset for CA and CB due to the different number of bound deuterons which affect the value of the carbon to different degree.

Prossi at 19:20, 20 November 2009

2009-11-20T19:20:11Z

← Older revision		Revision as of 19:20, 20 November 2009
Line 1:		Line 1:
	== '''Introduction''' ==		== '''Introduction''' ==

	Linear analysis of chemical shift ([http://www.ncbi.nlm.nih.gov/pubmed/16041479 LACS]) provides an independent means for absolute [[~~Www~~.bmrb.wisc.edu/iupac.pdf\|referencing]] of protein chemical shifts.  LACS is routinely run on all chemical shift sets submitted to the BioMagResBank (BMRB).		Linear analysis of chemical shift ([http://www.ncbi.nlm.nih.gov/pubmed/16041479 LACS]) provides an independent means for absolute [[www.bmrb.wisc.edu/iupac.pdf\|referencing]] of protein chemical shifts.  LACS is routinely run on all chemical shift sets submitted to the BioMagResBank (BMRB).

	In the contest of protein structure determination chemical shifts (CS) play a key role as reporters of secondary structure.  Backbone chemical shift derived dihedral angles can be obtained through programs such as [http://www.ncbi.nlm.nih.gov/pubmed/19548092 TALOS+] and are used as constraints in the structure determination process. The backbone shift set (CA, CB, CO, HN, N, HA) is also used in the molecular fragment selection (MFR) for [http://www.ncbi.nlm.nih.gov/pubmed/18326625 CS-Rosetta] structure prediction protocol.  Here fragments are selected from the protein databank (PDB) that have the same predicted CS as the query sequence.  Successful use of chemical shift for secondary structure inference requires the correct referencing.  The LACS server gives independent CS offsets for CA, CB, CO and HA and allows for effective correction of chemical shift sets derived from [''U''-<sup>13</sup>C,<sup>15</sup>N] and from [''U''-<sup>2</sup>H,<sup>13</sup>C,<sup>15</sup>N].  The latter labeling scheme may show distinct degrees of offset for CA and CB due to the different number of bound deuterons which affect the value of the carbon to different degree.		In the contest of protein structure determination chemical shifts (CS) play a key role as reporters of secondary structure.  Backbone chemical shift derived dihedral angles can be obtained through programs such as [http://www.ncbi.nlm.nih.gov/pubmed/19548092 TALOS+] and are used as constraints in the structure determination process. The backbone shift set (CA, CB, CO, HN, N, HA) is also used in the molecular fragment selection (MFR) for [http://www.ncbi.nlm.nih.gov/pubmed/18326625 CS-Rosetta] structure prediction protocol.  Here fragments are selected from the protein databank (PDB) that have the same predicted CS as the query sequence.  Successful use of chemical shift for secondary structure inference requires the correct referencing.  The LACS server gives independent CS offsets for CA, CB, CO and HA and allows for effective correction of chemical shift sets derived from [''U''-<sup>13</sup>C,<sup>15</sup>N] and from [''U''-<sup>2</sup>H,<sup>13</sup>C,<sup>15</sup>N].  The latter labeling scheme may show distinct degrees of offset for CA and CB due to the different number of bound deuterons which affect the value of the carbon to different degree.
Line 19:		Line 19:
	<br>		<br>

	A running [[Media:WR73-ILVFY_111809_4LACS.bmrb\|bmrb]] file and text [[~~media~~:LACS_output.txt\|output]] example are provided for user's convenience, adhering to the format should provide smooth operation of the server.<br>		A running [[Media:WR73-ILVFY_111809_4LACS.bmrb\|bmrb]] file and text [[Media:LACS_output.txt\|output]] example are provided for user's convenience, adhering to the format should provide smooth operation of the server.<br>

	<br>		<br>

Prossi at 19:18, 20 November 2009

2009-11-20T19:18:58Z

← Older revision		Revision as of 19:18, 20 November 2009
Line 19:		Line 19:
	<br>		<br>

	A running [[~~media~~:WR73-ILVFY_111809_4LACS.bmrb\|bmrb]] file and text output example are provided for user's convenience, adhering to the format should provide smooth operation of the server.<br>		A running [[Media:WR73-ILVFY_111809_4LACS.bmrb\|bmrb]] file and text [[media:LACS_output.txt\|output]] example are provided for user's convenience, adhering to the format should provide smooth operation of the server.<br>

	<br>		<br>
Line 90:		Line 90:

	</pre>		</pre>
	<br>		<br>

	== '''Practical Experience with Running LACS in the NESG''' ==		== '''Practical Experience with Running LACS in the NESG''' ==

Prossi at 19:18, 20 November 2009

2009-11-20T19:18:11Z

← Older revision		Revision as of 19:18, 20 November 2009
Line 19:		Line 19:
	<br>		<br>

	A running bmrb file and text output example are provided for user's convenience, adhering to the format should provide smooth operation of the server.<br>		A running [[media:WR73-ILVFY_111809_4LACS.bmrb\|bmrb]] file and text output example are provided for user's convenience, adhering to the format should provide smooth operation of the server.<br>


			<br>

	=== Example BMRB input for LACS ===		=== Example BMRB input for LACS ===
Line 51:		Line 51:

	</pre>		</pre>
			<br>

	=== Example LACS ouput ===		=== Example LACS ouput ===
Line 90:		Line 90:

	</pre>		</pre>
	<br>		<br>

	== '''Practical Experience with Running LACS in the NESG''' ==		== '''Practical Experience with Running LACS in the NESG''' ==

Prossi at 19:13, 20 November 2009

2009-11-20T19:13:46Z

← Older revision		Revision as of 19:13, 20 November 2009
Line 1:		Line 1:
	== '''Introduction''' ==		== '''Introduction''' ==

	Linear analysis of chemical shift ([http://www.ncbi.nlm.nih.gov/pubmed/16041479 LACS]) provides an independent means for absolute [[Www.bmrb.wisc.edu/iupac.pdf\|referencing]] of protein chemical shifts.  LACS is routinely run on all chemical shift sets submitted to the BioMagResBank (BMRB).		Linear analysis of chemical shift ([http://www.ncbi.nlm.nih.gov/pubmed/16041479 LACS]) provides an independent means for absolute [[Www.bmrb.wisc.edu/iupac.pdf\|referencing]] of protein chemical shifts.  LACS is routinely run on all chemical shift sets submitted to the BioMagResBank (BMRB).
Line 5:		Line 5:
	In the contest of protein structure determination chemical shifts (CS) play a key role as reporters of secondary structure.  Backbone chemical shift derived dihedral angles can be obtained through programs such as [http://www.ncbi.nlm.nih.gov/pubmed/19548092 TALOS+] and are used as constraints in the structure determination process. The backbone shift set (CA, CB, CO, HN, N, HA) is also used in the molecular fragment selection (MFR) for [http://www.ncbi.nlm.nih.gov/pubmed/18326625 CS-Rosetta] structure prediction protocol.  Here fragments are selected from the protein databank (PDB) that have the same predicted CS as the query sequence.  Successful use of chemical shift for secondary structure inference requires the correct referencing.  The LACS server gives independent CS offsets for CA, CB, CO and HA and allows for effective correction of chemical shift sets derived from [''U''-<sup>13</sup>C,<sup>15</sup>N] and from [''U''-<sup>2</sup>H,<sup>13</sup>C,<sup>15</sup>N].  The latter labeling scheme may show distinct degrees of offset for CA and CB due to the different number of bound deuterons which affect the value of the carbon to different degree.		In the contest of protein structure determination chemical shifts (CS) play a key role as reporters of secondary structure.  Backbone chemical shift derived dihedral angles can be obtained through programs such as [http://www.ncbi.nlm.nih.gov/pubmed/19548092 TALOS+] and are used as constraints in the structure determination process. The backbone shift set (CA, CB, CO, HN, N, HA) is also used in the molecular fragment selection (MFR) for [http://www.ncbi.nlm.nih.gov/pubmed/18326625 CS-Rosetta] structure prediction protocol.  Here fragments are selected from the protein databank (PDB) that have the same predicted CS as the query sequence.  Successful use of chemical shift for secondary structure inference requires the correct referencing.  The LACS server gives independent CS offsets for CA, CB, CO and HA and allows for effective correction of chemical shift sets derived from [''U''-<sup>13</sup>C,<sup>15</sup>N] and from [''U''-<sup>2</sup>H,<sup>13</sup>C,<sup>15</sup>N].  The latter labeling scheme may show distinct degrees of offset for CA and CB due to the different number of bound deuterons which affect the value of the carbon to different degree.

			<br>

			== '''Running LACS''' ==
	== '''Running LACS''' ==

	LACS can be run on the native [http://bija.nmrfam.wisc.edu/MANI-LACS/ server] using an edited version of the chemical shift file in bmrb 2.1 format, the user's email and project name.  The server returns the results very rapidly, the chemical shift file format is stringent and the output is of straight forward interpretation.		LACS can be run on the native [http://bija.nmrfam.wisc.edu/MANI-LACS/ server] using an edited version of the chemical shift file in bmrb 2.1 format, the user's email and project name.  The server returns the results very rapidly, the chemical shift file format is stringent and the output is of straight forward interpretation.
Line 21:		Line 21:
	A running bmrb file and text output example are provided for user's convenience, adhering to the format should provide smooth operation of the server.<br>		A running bmrb file and text output example are provided for user's convenience, adhering to the format should provide smooth operation of the server.<br>

	Example BMRB input for LACS:

			=== Example BMRB input for LACS ===
	<pre> _Mol_residue_sequence		<pre> _Mol_residue_sequence
	;		;
Line 48:		Line 50:


	</pre>		</pre>
	Example LACS ouput:

			=== Example LACS ouput ===

	The CA correction of -0.19 ppm is found (last line).		The CA correction of -0.19 ppm is found (last line).
	<pre>data_LACS		<pre>data_LACS

Line 85:		Line 89:
	_LACS_plot.Y_axis_chem_shift_offset -0.19		_LACS_plot.Y_axis_chem_shift_offset -0.19

	</pre>		</pre>
			<br>

			== '''Practical Experience with Running LACS in the NESG''' ==
	== '''Practical Experience with Running LACS in the NESG''' ==

	In the NESG the IUPAC referencing is obtained using internal 50 uM DSS and setting the DSS methyl peak to 0.00 ppm at the temperature of interest.  The spectrometer temperature is calibrated using a neat methanol sample in the 10 - 40 °C range.  Under these conditions, backbone CS of double labeled protein samples derived from triple resonance experiments alone typically show small deviations 0.1 - 0.3 ppm in <sup>13</sup>C and 0.01 - 0.03 ppm in <sup>1</sup>H.  The final CS set derived from double labeled samples filtered through higher resolution [<sup>1</sup>H,<sup>13</sup>C]-HSQC tends to give offsets at the lower extreme of this range.  On a smaller statistical sampling of triply labeled proteins we found higher offset values (0.4 - 0.8 ppm) in CA and CB.  Offsett correction prior to TALOS or MFR runs are therefore highly recommended especially for the treatment of triply labeled samples.		In the NESG the IUPAC referencing is obtained using internal 50 uM DSS and setting the DSS methyl peak to 0.00 ppm at the temperature of interest.  The spectrometer temperature is calibrated using a neat methanol sample in the 10 - 40 °C range.  Under these conditions, backbone CS of double labeled protein samples derived from triple resonance experiments alone typically show small deviations 0.1 - 0.3 ppm in <sup>13</sup>C and 0.01 - 0.03 ppm in <sup>1</sup>H.  The final CS set derived from double labeled samples filtered through higher resolution [<sup>1</sup>H,<sup>13</sup>C]-HSQC tends to give offsets at the lower extreme of this range.  On a smaller statistical sampling of triply labeled proteins we found higher offset values (0.4 - 0.8 ppm) in CA and CB.  Offsett correction prior to TALOS or MFR runs are therefore highly recommended especially for the treatment of triply labeled samples.
Line 98:		Line 102:
	editing of this entry is in progress (prossi)<br>		editing of this entry is in progress (prossi)<br>

			<br>

			<br>


	-- PaoloRossi - 20 Nov 2009		-- PaoloRossi - 20 Nov 2009

Prossi at 19:12, 20 November 2009

2009-11-20T19:12:08Z

@@ Line 1: / Line 1: @@
-Linear analysis of chemical shift ([http://www.ncbi.nlm.nih.gov/pubmed/16041479 LACS]) provides an independent means for absolute [[Www.bmrb.wisc.edu/iupac.pdf|referencing]] of protein chemical shifts.&nbsp; LACS is routinely run on all chemical shift sets submitted to the BioMagResBank (BMRB) &nbsp; In the contest of protein structure determination chemical shifts (CS) play a key role as reporters of secondary structure.&nbsp; Backbone chemical shift derived dihedral angles can be obtained through programs such as [http://www.ncbi.nlm.nih.gov/pubmed/19548092 TALOS+] and are used as constraints in the structure determination process. The backbone shift set (CA, CB, CO, HN, N, HA) is also used in the molecular fragment selection (MFR) for [http://www.ncbi.nlm.nih.gov/pubmed/18326625 CS-Rosetta] structure prediction protocol.&nbsp; Here fragments are selected from the protein databank (PDB) that have the same predicted CS as the query sequence.&nbsp; Therefore, successful use of chemical shift for secondary structure inference requires the correct referencing.&nbsp; LACS server gives independent CS offsets for CA, CB, CO and HA and allows for effective correction of chemical shift sets derived from [U-<sup>13</sup>C,<sup>15</sup>N] and from [U-<sup>2</sup>H,<sup>13</sup>C,<sup>15</sup>N].&nbsp; The latter labeling scheme may show distinct degrees of offset for CA and CB due to the number of bound deuterons. &nbsp;&nbsp;
+== '''Introduction''' ==
-LACS&nbsp;can be run on the native [http://bija.nmrfam.wisc.edu/MANI-LACS/ server] using a chemical shift file in bmrb 2.1 format and the user's email and project name.&nbsp; The server returns the results very rapidly, the chemical shift file format is stringent and the output is of straight forward interpretation.&nbsp;
+Linear analysis of chemical shift ([http://www.ncbi.nlm.nih.gov/pubmed/16041479 LACS]) provides an independent means for absolute [[Www.bmrb.wisc.edu/iupac.pdf|referencing]] of protein chemical shifts.&nbsp; LACS is routinely run on all chemical shift sets submitted to the BioMagResBank (BMRB).&nbsp;
-The items returned are:
+In the contest of protein structure determination chemical shifts (CS) play a key role as reporters of secondary structure.&nbsp; Backbone chemical shift derived dihedral angles can be obtained through programs such as [http://www.ncbi.nlm.nih.gov/pubmed/19548092 TALOS+] and are used as constraints in the structure determination process. The backbone shift set (CA, CB, CO, HN, N, HA) is also used in the molecular fragment selection (MFR) for [http://www.ncbi.nlm.nih.gov/pubmed/18326625 CS-Rosetta] structure prediction protocol.&nbsp; Here fragments are selected from the protein databank (PDB) that have the same predicted CS as the query sequence.&nbsp; Successful use of chemical shift for secondary structure inference requires the correct referencing.&nbsp; The LACS server gives independent CS offsets for CA, CB, CO and HA and allows for effective correction of chemical shift sets derived from [''U''-<sup>13</sup>C,<sup>15</sup>N] and from [''U''-<sup>2</sup>H,<sup>13</sup>C,<sup>15</sup>N].&nbsp; The latter labeling scheme may show distinct degrees of offset for CA and CB due to the different number of bound deuterons which affect the value of the carbon to different degree. &nbsp;&nbsp;
 i) a text file with the nucleus specific offsets from the linear fit of the secondary CS&nbsp; (e. g. deltaCA vs. deltaCA-deltaCB), obtained by subtracting the random coil value from the atom of interest.
@@ Line 9: / Line 17: @@
 ii) plots of the secondary CS outliers that may reveal incorrectly assigned residues.
-A running bmrb file and text output example are provided for user's convenience, adhering to the format should provide smooth operation of the server.
+== '''Practical Experience with Running LACS in the NESG''' ==
-<br>
+In the NESG the IUPAC&nbsp;referencing is obtained using internal 50 uM DSS and setting the DSS&nbsp;methyl peak to 0.00 ppm at the temperature of interest.&nbsp; The spectrometer temperature is calibrated using a neat methanol sample in the 10 - 40 °C range.&nbsp; Under these conditions, backbone CS of double labeled protein samples derived from triple resonance experiments alone typically show small deviations 0.1 - 0.3 ppm in <sup>13</sup>C and 0.01 - 0.03 ppm in <sup>1</sup>H.&nbsp; The final CS set derived from double labeled samples filtered through higher resolution [<sup>1</sup>H,<sup>13</sup>C]-HSQC tends to give offsets at the lower extreme of this range.&nbsp; On a smaller statistical sampling of triply labeled proteins we found higher offset values (0.4 - 0.8 ppm) in CA and CB.&nbsp; Offsett correction prior to TALOS&nbsp;or MFR runs are therefore highly recommended especially for the treatment of triply labeled samples. &nbsp;
 <br>
-<br>
+editing of this entry is in progress (prossi)<br>
-editing of this entry is in progress (prossi)<br>
+-- PaoloRossi - 20 Nov 2009