Resonance Assignment/Abacus/Introduction to ABACUS - Revision history

RyanDoherty at 21:39, 6 January 2010

2010-01-06T21:39:28Z

← Older revision		Revision as of 21:39, 6 January 2010
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	= FMC Graphical User Interface =		= FMC Graphical User Interface =
	<div>FMCGUI is a graphical interface that allows the user to carry out resonance assignment and structure calculation using the ABACUS approach.  FMCGUI integrates a number of FORTRAN applications: controlling the data-flow between the applications, executing applications, and visualizing data for effective analysis of results. <br></div><div></div><div>The main purpose of FMCGUI is to provide an interactive tool for resonance assignment.  FMCGUI includes a structure calculation component, which can be used independently from the resonance assignment component.  The structure calculation component assists the user by setting up structure calculations with CYANA, water refinement calculations with CNS, and performs an analysis of their results.  ~~NOTE:~~ The structure calculations are to be run externally from FMCGUI, on a linux cluster. </div>		<div>FMCGUI is a graphical interface that allows the user to carry out resonance assignment and structure calculation using the ABACUS approach.  FMCGUI integrates a number of FORTRAN applications: controlling the data-flow between the applications, executing applications, and visualizing data for effective analysis of results. <br></div><div></div><div>The main purpose of FMCGUI is to provide an interactive tool for resonance assignment.  FMCGUI includes a structure calculation component, which can be used independently from the resonance assignment component.  The structure calculation component assists the user by setting up structure calculations with CYANA, water refinement calculations with CNS, and performs an analysis of their results.  The structure calculations are to be run externally from FMCGUI, on a linux cluster. </div>

RyanDoherty at 21:39, 6 January 2010

2010-01-06T21:39:10Z

← Older revision		Revision as of 21:39, 6 January 2010
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	= FMC Graphical User Interface =		= FMC Graphical User Interface =
	<div>FMCGUI is a graphical interface that allows the user to carry out resonance assignment and structure calculation using the ABACUS approach. FMCGUI integrates a number of FORTRAN applications: controlling the data-flow between the applications, executing applications, and visualizing data for effective analysis of results. <br></div><div>The main purpose of FMCGUI is to provide an interactive tool for resonance assignment.~~</div><div>Structural part of~~ FMCGUI can be used  independently from the resonance assignment ~~part~~. ~~It helps to set~~ up ~~both~~ structure calculations with ~~CAYNA and~~ water refinement calculations with CNS and ~~to analyse~~ results. The ~~actual~~ structure calculations are ~~supposed~~ to be ~~carried out outside~~ FMCGUI on linux cluster. </div>		<div>FMCGUI is a graphical interface that allows the user to carry out resonance assignment and structure calculation using the ABACUS approach.  FMCGUI integrates a number of FORTRAN applications: controlling the data-flow between the applications, executing applications, and visualizing data for effective analysis of results. <br></div><div></div><div>The main purpose of FMCGUI is to provide an interactive tool for resonance assignment.  FMCGUI includes a structure calculation component, which can be used independently from the resonance assignment component.  The structure calculation component assists the user by setting up structure calculations with CYANA, water refinement calculations with CNS, and performs an analysis of their results.  NOTE: The structure calculations are to be run externally from FMCGUI, on a linux cluster. </div>

RyanDoherty at 21:32, 6 January 2010

2010-01-06T21:32:37Z

← Older revision		Revision as of 21:32, 6 January 2010
Line 139:		Line 139:

	= FMC Graphical User Interface =		= FMC Graphical User Interface =
	<div>FMCGUI is a graphical interface that ~~assist~~ user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI ~~integrate~~ a number of FORTRAN applications: ~~performs control of~~ the data-flow between the applications, ~~execute the~~ applications, and ~~helps to analyze effectively obtained results by~~ visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>		<div>FMCGUI is a graphical interface that allows the user to carry out resonance assignment and structure calculation using the ABACUS approach. FMCGUI integrates a number of FORTRAN applications: controlling the data-flow between the applications, executing applications, and visualizing data for effective analysis of results. <br></div><div>The main purpose of FMCGUI is to provide an interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used  independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

RyanDoherty at 21:28, 6 January 2010

2010-01-06T21:28:41Z

@@ Line 135: / Line 135: @@
 <div>[[Image:Fmcgui Fig1.3.jpg|thumb|center|600px]]</div><div></div><div></div><div>&nbsp;FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations. &nbsp;Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none">&nbsp;</span>k = 1,….,N<sub>f.&nbsp;;</sub>''</div>
 ==== Figure 1.4<br> ====
-<br>
+[[Image:Fmcgui Fig1.4.jpg|thumb|center|600px]]&nbsp;
 = FMC Graphical User Interface  =
 <div>FMCGUI is a graphical interface that assist user to carry out resonance assignment and structure calculation using ABACUS approach. FMCGUI integrate a number of FORTRAN applications: performs control of the data-flow between the applications, execute the applications, and helps to analyze effectively obtained results by visualizing data. <br></div><div>The main purpose of FMCGUI is to provide interactive tool for resonance assignment.</div><div>Structural part of FMCGUI can be used&nbsp; independently from the resonance assignment part. It helps to set up both structure calculations with CAYNA and water refinement calculations with CNS and to analyse results. The actual structure calculations are supposed to be carried out outside FMCGUI on linux cluster. </div>

RyanDoherty at 21:28, 6 January 2010

2010-01-06T21:28:20Z

← Older revision		Revision as of 21:28, 6 January 2010
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	<div>[[Image:Fmcgui Fig1.3.jpg\|thumb\|center\|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>		<div>[[Image:Fmcgui Fig1.3.jpg\|thumb\|center\|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
	==== Figure 1.4<br> ====		==== Figure 1.4<br> ====
	~~<center>~~		[[Image:Fmcgui Fig1.4.jpg\|thumb\|center\|600px]]
	[[Image:Fmcgui Fig1.4.jpg\|thumb\|~~left~~\|600px]] ~~</center>~~

	<br>		<br>

RyanDoherty at 21:27, 6 January 2010

2010-01-06T21:27:43Z

← Older revision		Revision as of 21:27, 6 January 2010
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	<div>[[Image:Fmcgui Fig1.3.jpg\|thumb\|center\|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>		<div>[[Image:Fmcgui Fig1.3.jpg\|thumb\|center\|600px]]</div><div></div><div></div><div> FMC procedure performs ''<u>probabilistic assignment</u>'' of PB-fragments. The assignment probabilities <span>P<sub>s</sub><sup>k</sup></span><span> are calculated by Simulated Annealing (SA) or Replica Exchange Method (REM) Monte Carlo (MC) simulations.  Here, P<sub>s</sub><sup>k</sup> is a </span>probability of fragment ''k'' to occupy position ''s;'<span id="1259188877701S" style="display: none"> </span>k = 1,….,N<sub>f. ;</sub>''</div>
	==== Figure 1.4<br> ====		==== Figure 1.4<br> ====
			<center>
	[[Image:Fmcgui Fig1.4.jpg\|thumb\|left\|600px]]		[[Image:Fmcgui Fig1.4.jpg\|thumb\|left\|600px]] </center>

	<br>		<br>

RyanDoherty at 21:26, 6 January 2010

2010-01-06T21:26:29Z

← Older revision		Revision as of 21:26, 6 January 2010
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	[[Image:PBfragment.jpg\|thumb\|right\|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>		[[Image:PBfragment.jpg\|thumb\|right\|440px]]Schematic description of two types of molecular fragments: traditional spin-system (AA-fragment)<span> include all the atoms belonging to the same residue; PB-fragment includes all the atoms from one residue except the backbone amide group, plus the amide group from the next residue in the protein</span>

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	</div><div></div>		</div><div></div>
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RyanDoherty at 21:26, 6 January 2010

2010-01-06T21:26:08Z

← Older revision		Revision as of 21:26, 6 January 2010
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	<br>		<br>

	~~==== ''~~ ~~'' ====~~		<br>

			<br>

	==== ''b''PB fragment ====		==== ''b''PB fragment ====

RyanDoherty at 21:25, 6 January 2010

2010-01-06T21:25:39Z

← Older revision		Revision as of 21:25, 6 January 2010
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	</div><div></div>		</div><div></div>
	<br>		<br>
	====
			==== '' '' ====

	==== ''b''PB fragment ====		==== ''b''PB fragment ====

RyanDoherty: /* == */

2010-01-06T21:25:23Z

← Older revision		Revision as of 21:25, 6 January 2010
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	</div><div></div>		</div><div></div>
	<br>		<br>
	~~====~~
	====		====