Resonance Assignment/Abacus/FMCGUI objects - Revision history

RyanDoherty at 00:23, 9 January 2010

2010-01-09T00:23:55Z

← Older revision		Revision as of 00:23, 9 January 2010
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	<span>T<sup>t </sup>(f)  </span><span>is a probability for fragment ''f ''to have amino acid type ''t''</span><span>. Here ''t ''corresponds to one of 20 amino acid residue types, and f </span><span>is fragment user ID. </span>		<span>T<sup>t </sup>(f)  </span><span>is a probability for fragment ''f ''to have amino acid type ''t''</span><span>. Here ''t ''corresponds to one of 20 amino acid residue types, and f </span><span>is fragment user ID. </span>

	Typing probbilities  ~~could~~ be calculated or modified manually by the commands {[[FMCGUI commands#Fragment.3EType.3ECalculate.3E\|Fragment>Type>Calculate]]} and  {[[FMCGUI commands#Fragment.3EType.3Efix\|Fragment>Type>Fix]]}, respectively.		Typing probbilities can be calculated or modified manually by the commands {[[FMCGUI commands#Fragment.3EType.3ECalculate.3E\|Fragment>Type>Calculate]]} and  {[[FMCGUI commands#Fragment.3EType.3Efix\|Fragment>Type>Fix]]}, respectively.

	==== Contact map ====		==== Contact map ====

RyanDoherty at 20:54, 8 January 2010

2010-01-08T20:54:41Z

Show changes

Agutmana: moved FMCGUI objects to Resonance Assignment/Abacus/FMCGUI objects

2010-01-05T23:33:15Z

moved FMCGUI objects to Resonance Assignment/Abacus/FMCGUI objects

← Older revision	Revision as of 23:33, 5 January 2010
(No difference)

AlexLemak at 14:48, 3 December 2009

2009-12-03T14:48:06Z

← Older revision		Revision as of 14:48, 3 December 2009
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	<div></div>		<div></div>
	==== Figure 2.1 ====		==== Figure 2.1 ====
	<div></div><div>[[Image:Fmcgui mainwindow.jpg\|thumb\|left\|500px]]</div><div></div><div></div><div></div><div></div><div><br><br><br><br><br><br><br><br><br><br><br><br></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div>The main frame of FMC Graphical Interface consist of 4 sections (see Figure ~~2.1~~)<br></div>		<div></div><div>[[Image:Fmcgui mainwindow.jpg\|thumb\|left\|500px]]</div><div></div><div></div><div></div><div></div><div><br><br><br><br><br><br><br><br><br><br><br><br></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div>The main frame of FMC Graphical Interface consist of 4 sections (see Figure)<br></div>
	* the title bar displays the name of the current project and the directory inside which the project is located;		* the title bar displays the name of the current project and the directory inside which the project is located;
	* the bar with six menus: [[FMCGUI commands#Project_Menu\|Project]], [[FMCGUI commands#Data_Menu\|Data]], [[FMCGUI commands#Fragment_menu\|Fragment]], [[FMCGUI commands#Assignment_menu\|Assignment]], [[FMCGUI commands#Structure_menu\|Structure]], and [[FMCGUI commands#View_menu\|View]], respectively;		* the bar with six menus: [[FMCGUI commands#Project_Menu\|Project]], [[FMCGUI commands#Data_Menu\|Data]], [[FMCGUI commands#Fragment_menu\|Fragment]], [[FMCGUI commands#Assignment_menu\|Assignment]], [[FMCGUI commands#Structure_menu\|Structure]], and [[FMCGUI commands#View_menu\|View]], respectively;

AlexLemak at 14:47, 3 December 2009

2009-12-03T14:47:27Z

← Older revision		Revision as of 14:47, 3 December 2009
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	==== Contact map ====		==== Contact map ====

	:There are three fragment contact maps: C<sup>f1</sup><sub>HNCA</sub><span>(f2)  , </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) ,</span><span>  and </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2) </span><span>, respectively. Each contact map scores the possibility for any fragment ''f1'' to be next to the fragment ''f1'' in protein sequence. Here ''f''1 and ''f2'' stand for fragment's user ID. </span>		:There are three fragment contact maps: C<sup>f1</sup><sub>HNCA</sub><span>(f2)  , </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) ,</span><span>  and </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2) </span><span>, respectively. Each contact map scores the possibility for any fragment ''f1'' to be next to the fragment ''f2'' in protein sequence. Here ''f''1 and ''f2'' stand for fragment's user ID. </span>
	<div><span> Fragment contact map  </span>C<sup>f1</sup><sub>HNCA</sub><span>(f2) </span><span>is calculated based on HNCA spectrum by the command   {[[FMCGUI commands#Assignment.3EContacts.3EHNCA\|Assignment>Contacts>HNCA]]}<div> Fragment<span>   contact maps </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) </span><span>  and </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2) </span>~~<span />~~<span>  are calculated from NOESY spectra with or without using BACUS procedure, respectively.</span></div><div><span>  </span><span> </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2)  </span><span> can be calculated for all values of f1 and f2 by both commands   {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Efawn\|Assignment>Contacts>NOE>fawn]]}   and {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus\|Assignment>Contact>NOE>abacus]]}, while   </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) </span>~~<span />~~<span> is calculated by  command {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus\|Assignment>Contact>NOE>abacus]]}.<div> </div></span></div></span></div>		<div><span> Fragment contact map  </span>C<sup>f1</sup><sub>HNCA</sub><span>(f2) </span><span>is calculated based on HNCA spectrum by the command   {[[FMCGUI commands#Assignment.3EContacts.3EHNCA\|Assignment>Contacts>HNCA]]}<div> Fragment<span>   contact maps </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) </span><span>  and </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2) </span><span>  are calculated from NOESY spectra with or without using BACUS procedure, respectively.</span></div><div><span>  </span><span> </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2)  </span><span> can be calculated for all values of f1 and f2 by both commands   {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Efawn\|Assignment>Contacts>NOE>fawn]]}   and {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus\|Assignment>Contact>NOE>abacus]]}, while   </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) </span><span> is calculated by  command {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus\|Assignment>Contact>NOE>abacus]]}.<div> </div></span></div></span></div>

	==== Assignment probabilities ====		==== Assignment probabilities ====

AlexLemak at 19:22, 1 December 2009

2009-12-01T19:22:07Z

← Older revision		Revision as of 19:22, 1 December 2009
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	== List of PB fragments ==		== List of PB fragments ==
	<div></div><div>This object can be created in memory using {[[FMCGUI commands#Fragment.3ELoad.3EPB_fragments\|Fragment>Load>]]}, {[[FMCGUI commands#Fragment.3ECreate.3Eabacus\|Fragment>Create>abacus]]}, or {[[FMCGUI commands#Project.3ELoad\|Project>Load]]} commands. </div><div></div><div>Each PB fragment in the list has the following main properties:</div>		<div></div><div>This object can be created in memory using {[[FMCGUI commands#Fragment.3ELoad.3EPB_fragments\|Fragment>Load>]]}, {[[FMCGUI commands#Fragment.3ECreate.3Eabacus\|Fragment>Create>abacus]]}, or {[[FMCGUI commands#Project.3ELoad\|Project>Load]]} commands. </div><div></div><div>Each PB fragment in the list has the following main properties:</div>
	==== User ID~~    ~~       ====		==== User ID       ====

	Fragment ID assigned by user, ''U_id''<span style="font-style: italic;">. </span>''U_id'' can’t be changed within FMCGUI.		Fragment ID assigned by user, ''U_id''<span style="font-style: italic;">. </span>''U_id'' can’t be changed within FMCGUI.

	==== Assignment ID ====		==== Assignment ID ====

AlexLemak at 16:35, 1 December 2009

2009-12-01T16:35:32Z

← Older revision		Revision as of 16:35, 1 December 2009
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	Typing probbilities  could be calculated or modified manually by the commands {[[FMCGUI commands#Fragment.3EType.3ECalculate.3E\|Fragment>Type>Calculate]]} and  {[[FMCGUI commands#Fragment.3EType.3Efix\|Fragment>Type>Fix]]}, respectively.		Typing probbilities  could be calculated or modified manually by the commands {[[FMCGUI commands#Fragment.3EType.3ECalculate.3E\|Fragment>Type>Calculate]]} and  {[[FMCGUI commands#Fragment.3EType.3Efix\|Fragment>Type>Fix]]}, respectively.

	=== Contact map ===		==== Contact map ====

	:There are three fragment contact maps: C<sup>f1</sup><sub>HNCA</sub><span>(f2)  , </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) ,</span><span>  and </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2) </span><span>, respectively. Each contact map scores the possibility for any fragment ''f1'' to be next to the fragment ''f1'' in protein sequence. Here ''f''1 and ''f2'' stand for fragment's user ID. </span>		:There are three fragment contact maps: C<sup>f1</sup><sub>HNCA</sub><span>(f2)  , </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) ,</span><span>  and </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2) </span><span>, respectively. Each contact map scores the possibility for any fragment ''f1'' to be next to the fragment ''f1'' in protein sequence. Here ''f''1 and ''f2'' stand for fragment's user ID. </span>
	<div><span> Fragment contact map  </span>C<sup>f1</sup><sub>HNCA</sub><span>(f2) </span><span>is calculated based on HNCA spectrum by the command   {[[FMCGUI commands#Assignment.3EContacts.3EHNCA\|Assignment>Contacts>HNCA]]}<div> Fragment<span>   contact maps </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) </span><span>  and </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2) </span><span /><span>  are calculated from NOESY spectra with or without using BACUS procedure, respectively.</span></div><div><span>  </span><span> </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2)  </span><span> can be calculated for all values of f1 and f2 by both commands   {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Efawn\|Assignment>Contacts>NOE>fawn]]}   and {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus\|Assignment>Contact>NOE>abacus]]}, while   </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) </span><span /><span> is calculated by  command {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus\|Assignment>Contact>NOE>abacus]]}.<div> </div></span></div></span></div>		<div><span> Fragment contact map  </span>C<sup>f1</sup><sub>HNCA</sub><span>(f2) </span><span>is calculated based on HNCA spectrum by the command   {[[FMCGUI commands#Assignment.3EContacts.3EHNCA\|Assignment>Contacts>HNCA]]}<div> Fragment<span>   contact maps </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) </span><span>  and </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2) </span><span /><span>  are calculated from NOESY spectra with or without using BACUS procedure, respectively.</span></div><div><span>  </span><span> </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2)  </span><span> can be calculated for all values of f1 and f2 by both commands   {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Efawn\|Assignment>Contacts>NOE>fawn]]}   and {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus\|Assignment>Contact>NOE>abacus]]}, while   </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) </span><span /><span> is calculated by  command {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus\|Assignment>Contact>NOE>abacus]]}.<div> </div></span></div></span></div>
			==== Assignment probabilities ====
	=== Assignment probabilities ===

	:		:
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	<br>		<br>
	<div> <span>P<sup>s</sup><sub>SA</sub>(f)    is calclated by command {[[FMCGUI commands#Assignment.3ECalculate_Probabilities.3ESA\|Assignment>Calculate Probabilities>SA]]}  </span><br></div><div>''' '''<span>P<sup>s</sup><sub>REM</sub>(f)  is calculated by command {[[FMCGUI commands#Assignment.3ECalculate_Probabilities.3EREM\|Assignment>Calculate probabilities>REM]]}.</span></div><div><br></div><div><span>Both assignment probabilities could be also  loaded in memory from already performed calculations using command {[[FMCGUI commands#Assignment.3ELoad_Probabilities\|Assignment>Load probabilities]]}.</span></div><div> </div><div>'''<br>'''</div>		<div> <span>P<sup>s</sup><sub>SA</sub>(f)    is calclated by command {[[FMCGUI commands#Assignment.3ECalculate_Probabilities.3ESA\|Assignment>Calculate Probabilities>SA]]}  </span><br></div><div>''' '''<span>P<sup>s</sup><sub>REM</sub>(f)  is calculated by command {[[FMCGUI commands#Assignment.3ECalculate_Probabilities.3EREM\|Assignment>Calculate probabilities>REM]]}.</span></div><div><br></div><div><span>Both assignment probabilities could be also  loaded in memory from already performed calculations using command {[[FMCGUI commands#Assignment.3ELoad_Probabilities\|Assignment>Load probabilities]]}.</span></div><div> </div><div>'''<br>'''</div>

	== Main window ==		== Main window ==
	<div></div>		<div></div>

AlexLemak at 16:11, 1 December 2009

2009-12-01T16:11:31Z

← Older revision		Revision as of 16:11, 1 December 2009
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	=== Contact map ===		=== Contact map ===

	:There are three fragment contact maps: C<sup>f1</sup><sub>CA</sub><span>(f2)  , </span>C<sup>f1</sup><sub>B</sub><span>(f2) ,</span><span>  and </span>C<sup>f1</sup><sub>F</sub><span>(f2) </span><span>, respectively. Each contact map scores the possibility for any fragment ''f1'' to be next to the fragment ''f1'' in protein sequence. Here ''f''1 and ''f2'' stand for fragment's user ID. </span>		:There are three fragment contact maps: C<sup>f1</sup><sub>HNCA</sub><span>(f2)  , </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) ,</span><span>  and </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2) </span><span>, respectively. Each contact map scores the possibility for any fragment ''f1'' to be next to the fragment ''f1'' in protein sequence. Here ''f''1 and ''f2'' stand for fragment's user ID. </span>
	<div><span> Fragment contact map  </span>C<sup>f1</sup><sub>CA</sub><span>(f2) </span><span>is calculated based on HNCA spectrum by the command   {[[FMCGUI commands#Assignment.3EContacts.3EHNCA\|Assignment>Contacts>HNCA]]}<div> Fragment<span>   contact maps </span>C<sup>f1</sup><sub>B</sub><span>(f2) </span><span>  and </span>C<sup>f1</sup><sub>F</sub><span>(f2) </span><span /><span>  are calculated from NOESY spectra with or without using BACUS procedure, respectively.</span></div><div><span>  </span><span> </span>C<sup>f1</sup><sub>F</sub><span>(f2)  </span><span> can be calculated for all values of f1 and f2 by both commands   {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Efawn\|Assignment>Contacts>NOE>fawn]]}   and {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus\|Assignment>Contact>NOE>abacus]]}, while   </span>C<sup>f1</sup><sub>B</sub><span>(f2) </span><span /><span> is calculated by  command {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus\|Assignment>Contact>NOE>abacus]]}.<div> </div></span></div></span></div>		<div><span> Fragment contact map  </span>C<sup>f1</sup><sub>HNCA</sub><span>(f2) </span><span>is calculated based on HNCA spectrum by the command   {[[FMCGUI commands#Assignment.3EContacts.3EHNCA\|Assignment>Contacts>HNCA]]}<div> Fragment<span>   contact maps </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) </span><span>  and </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2) </span><span /><span>  are calculated from NOESY spectra with or without using BACUS procedure, respectively.</span></div><div><span>  </span><span> </span>C<sup>f1</sup><sub>NOE_F</sub><span>(f2)  </span><span> can be calculated for all values of f1 and f2 by both commands   {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Efawn\|Assignment>Contacts>NOE>fawn]]}   and {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus\|Assignment>Contact>NOE>abacus]]}, while   </span>C<sup>f1</sup><sub>NOE_B</sub><span>(f2) </span><span /><span> is calculated by  command {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus\|Assignment>Contact>NOE>abacus]]}.<div> </div></span></div></span></div>

	=== Assignment probabilities ===		=== Assignment probabilities ===

AlexLemak at 22:52, 30 November 2009

2009-11-30T22:52:31Z

← Older revision		Revision as of 22:52, 30 November 2009
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	<div>Most of FMCGUI commands operate mainly with the following three objects that are located in computer memory: </div>		<div>Most of FMCGUI commands operate mainly with the following three objects that are located in computer memory: </div>
	*protein sequence		*protein sequence
	*peak list		*peak list
	*and PB fragments.		*and PB fragments.
	<div> </div>		<div> </div>
	== '''Protein sequence''' ==		== '''Protein sequence''' ==
	<div>This object can be created in memory using {[[FMCGUI commands#Data~~>Protein_Sequence>Load~~\|Data>Protein Sequence>Load ]]} or {[[FMCGUI commands#Project.3ELoad\|Project>Load]]} commands. <br></div><div> </div><div> The position ID of the first residue in the sequence should be specified by user upon loading sequence file (in the case it is not specified in the input file). Some commands in FMCGUI implies that the first residue of the protein sequence has position ID of 1. Therefore, if there is HIS-tag, then the loaded sequence should be numbered accordingly starting with a negative position ID of the first residue.</div><div> </div>		<div>This object can be created in memory using {[[FMCGUI commands#Data.3EProtein_Sequence.3ELoad\|Data>Protein Sequence>Load ]]} or {[[FMCGUI commands#Project.3ELoad\|Project>Load]]} commands. <br></div><div> </div><div> The position ID of the first residue in the sequence should be specified by user upon loading sequence file (in the case it is not specified in the input file). Some commands in FMCGUI implies that the first residue of the protein sequence has position ID of 1. Therefore, if there is HIS-tag, then the loaded sequence should be numbered accordingly starting with a negative position ID of the first residue.</div><div> </div>

	== Peak list ==		== Peak list ==
	<div>Different peak lists objects can be created in memory using {[[FMCGUI commands#Data.3EN15_NOESY.3E\|Data>”Peak list name”>Load]]} or {[[FMCGUI commands#Project.3ELoad\|Project>Load]]}</div><div></div><div></div><div><br> </div>		<div>Different peak lists objects can be created in memory using {[[FMCGUI commands#Data.3EN15_NOESY.3E\|Data>”Peak list name”>Load]]} or {[[FMCGUI commands#Project.3ELoad\|Project>Load]]}</div><div></div><div></div><div><br> </div>
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	\| width="88" valign="top" \| <div align="center">+</div>		\| width="88" valign="top" \| <div align="center">+</div>
	\|}		\|}
	<div align="center"><span>           </span></div><div> </div>		<div align="center"><span>           </span></div><div> </div>
			== List of PB fragments ==
	== ~~ ~~List of PB fragments ==
	<div></div><div>This object can be created in memory using {[[FMCGUI commands#Fragment.3ELoad.3EPB_fragments\|Fragment>Load>]]}, {[[FMCGUI commands#Fragment.3ECreate.3Eabacus\|Fragment>Create>abacus]]}, or {[[FMCGUI commands#Project.3ELoad\|Project>Load]]} commands. </div><div></div><div>Each PB fragment in the list has the following main properties:</div>		<div></div><div>This object can be created in memory using {[[FMCGUI commands#Fragment.3ELoad.3EPB_fragments\|Fragment>Load>]]}, {[[FMCGUI commands#Fragment.3ECreate.3Eabacus\|Fragment>Create>abacus]]}, or {[[FMCGUI commands#Project.3ELoad\|Project>Load]]} commands. </div><div></div><div>Each PB fragment in the list has the following main properties:</div>
	==== User ID           ====		==== User ID           ====

	Fragment ID assigned by user, ''U_id''<span style="font-style: italic;">. </span>''U_id'' can’t be changed within FMCGUI.		Fragment ID assigned by user, ''U_id''<span style="font-style: italic;">. </span>''U_id'' can’t be changed within FMCGUI.

	==== Assignment ID ====		==== Assignment ID ====
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	''A_id'' = -99 if the fragment is not assigned to any position in the sequence.		''A_id'' = -99 if the fragment is not assigned to any position in the sequence.

	''A_id'' could be set up or modified by the following commands {[[FMCGUI commands#Assignment.3EFix_Assignment.3EManually\|Assignment>Fix Assignment>Manually]]}, {[[FMCGUI commands#Assignment.3EFix_Assignment.3EUsing_Probability_map\|Assignment>Fix Assignment>Using probability Map]]}, and {[[FMCGUI commands#Assignment.3EFix_Assignment.3EReset_all\|Assignment>Fix Assignment>Reset all]] }.		''A_id'' could be set up or modified by the following commands {[[FMCGUI commands#Assignment.3EFix_Assignment.3EManually\|Assignment>Fix Assignment>Manually]]}, {[[FMCGUI commands#Assignment.3EFix_Assignment.3EUsing_Probability_map\|Assignment>Fix Assignment>Using probability Map]]}, and {[[FMCGUI commands#Assignment.3EFix_Assignment.3EReset_all\|Assignment>Fix Assignment>Reset all]] }.

	==== Typing probabilities ====		==== Typing probabilities ====
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	<span>T<sup>t </sup>(f)  </span><span>is a probability for fragment ''f ''to have amino acid type ''t''</span><span>. Here ''t ''corresponds to one of 20 amino acid residue types, and f </span><span>is fragment user ID. </span>		<span>T<sup>t </sup>(f)  </span><span>is a probability for fragment ''f ''to have amino acid type ''t''</span><span>. Here ''t ''corresponds to one of 20 amino acid residue types, and f </span><span>is fragment user ID. </span>

	Typing probbilities  could be calculated or modified manually by the commands {[[FMCGUI commands#Fragment.3EType.3ECalculate.3E\|Fragment>Type>Calculate]]} and  {[[FMCGUI commands#Fragment.3EType.3Efix\|Fragment>Type>Fix]]}, respectively.		Typing probbilities  could be calculated or modified manually by the commands {[[FMCGUI commands#Fragment.3EType.3ECalculate.3E\|Fragment>Type>Calculate]]} and  {[[FMCGUI commands#Fragment.3EType.3Efix\|Fragment>Type>Fix]]}, respectively.

	=== Contact map ===		=== Contact map ===

	:There are three fragment contact maps: C<sup>f1</sup><sub>CA</sub><span>(f2)  , </span>C<sup>f1</sup><sub>B</sub><span>(f2) ,</span><span>  and </span>C<sup>f1</sup><sub>F</sub><span>(f2) </span><span>, respectively. Each contact map scores the possibility for any fragment ''f1'' to be next to the fragment ''f1'' in protein sequence. Here ''f''1 and ''f2'' stand for fragment's user ID. </span>		:There are three fragment contact maps: C<sup>f1</sup><sub>CA</sub><span>(f2)  , </span>C<sup>f1</sup><sub>B</sub><span>(f2) ,</span><span>  and </span>C<sup>f1</sup><sub>F</sub><span>(f2) </span><span>, respectively. Each contact map scores the possibility for any fragment ''f1'' to be next to the fragment ''f1'' in protein sequence. Here ''f''1 and ''f2'' stand for fragment's user ID. </span>
	<div><span> Fragment contact map  </span>C<sup>f1</sup><sub>CA</sub><span>(f2) </span><span>is calculated based on HNCA spectrum by the command   {[[FMCGUI commands#Assignment.3EContacts.3EHNCA\|Assignment>Contacts>HNCA]]}<div> Fragment<span>   contact maps </span>C<sup>f1</sup><sub>B</sub><span>(f2) </span><span>  and </span>C<sup>f1</sup><sub>F</sub><span>(f2) </span><span /><span>  are calculated from NOESY spectra with or without using BACUS procedure, respectively.</span></div><div><span>  </span><span> </span>C<sup>f1</sup><sub>F</sub><span>(f2)  </span><span> can be calculated for all values of f1 and f2 by both commands   {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Efawn\|Assignment>Contacts>NOE>fawn]]}   and {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus\|Assignment>Contact>NOE>abacus]]}, while   </span>C<sup>f1</sup><sub>B</sub><span>(f2) </span><span /><span> is calculated by  command {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus\|Assignment>Contact>NOE>abacus]]}.<div> </div></span></div></span></div>		<div><span> Fragment contact map  </span>C<sup>f1</sup><sub>CA</sub><span>(f2) </span><span>is calculated based on HNCA spectrum by the command   {[[FMCGUI commands#Assignment.3EContacts.3EHNCA\|Assignment>Contacts>HNCA]]}<div> Fragment<span>   contact maps </span>C<sup>f1</sup><sub>B</sub><span>(f2) </span><span>  and </span>C<sup>f1</sup><sub>F</sub><span>(f2) </span><span /><span>  are calculated from NOESY spectra with or without using BACUS procedure, respectively.</span></div><div><span>  </span><span> </span>C<sup>f1</sup><sub>F</sub><span>(f2)  </span><span> can be calculated for all values of f1 and f2 by both commands   {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Efawn\|Assignment>Contacts>NOE>fawn]]}   and {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus\|Assignment>Contact>NOE>abacus]]}, while   </span>C<sup>f1</sup><sub>B</sub><span>(f2) </span><span /><span> is calculated by  command {[[FMCGUI commands#Assignment.3EContacts.3ENOE.3Eabacus\|Assignment>Contact>NOE>abacus]]}.<div> </div></span></div></span></div>

	=== Assignment probabilities ===		=== Assignment probabilities ===

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	<br>		<br>
	<div> <span>P<sup>s</sup><sub>SA</sub>(f)    is calclated by command {[[FMCGUI commands#Assignment.3ECalculate_Probabilities.3ESA\|Assignment>Calculate Probabilities>SA]]}  </span><br></div><div>''' '''<span>P<sup>s</sup><sub>REM</sub>(f)  is calculated by command {[[FMCGUI commands#Assignment.3ECalculate_Probabilities.3EREM\|Assignment>Calculate probabilities>REM]]}.</span></div><div><br></div><div><span>Both assignment probabilities could be also  loaded in memory from already performed calculations using command {[[FMCGUI commands#Assignment.3ELoad_Probabilities\|Assignment>Load probabilities]]}.</span></div><div> ~~</div><div><br></div><div>''' '''~~</div><div>'''~~ ~~<br>'''</div>		<div> <span>P<sup>s</sup><sub>SA</sub>(f)    is calclated by command {[[FMCGUI commands#Assignment.3ECalculate_Probabilities.3ESA\|Assignment>Calculate Probabilities>SA]]}  </span><br></div><div>''' '''<span>P<sup>s</sup><sub>REM</sub>(f)  is calculated by command {[[FMCGUI commands#Assignment.3ECalculate_Probabilities.3EREM\|Assignment>Calculate probabilities>REM]]}.</span></div><div><br></div><div><span>Both assignment probabilities could be also  loaded in memory from already performed calculations using command {[[FMCGUI commands#Assignment.3ELoad_Probabilities\|Assignment>Load probabilities]]}.</span></div><div> </div><div>'''<br>'''</div>

	== Main window ==		== Main window ==
	<div></div>		<div></div>
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	<div></div><div>[[Image:Fmcgui mainwindow.jpg\|thumb\|left\|500px]]</div><div></div><div></div><div></div><div></div><div><br><br><br><br><br><br><br><br><br><br><br><br></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div>The main frame of FMC Graphical Interface consist of 4 sections (see Figure 2.1)<br></div>		<div></div><div>[[Image:Fmcgui mainwindow.jpg\|thumb\|left\|500px]]</div><div></div><div></div><div></div><div></div><div><br><br><br><br><br><br><br><br><br><br><br><br></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div>The main frame of FMC Graphical Interface consist of 4 sections (see Figure 2.1)<br></div>
	* the title bar displays the name of the current project and the directory inside which the project is located;		* the title bar displays the name of the current project and the directory inside which the project is located;
	* the bar with six menus: [[FMCGUI commands#Project_Menu\|Project]], [[FMCGUI commands#Data_Menu\|Data]], [[FMCGUI commands#Fragment_menu\|Fragment]], [[FMCGUI commands#Assignment_menu\|Assignment]], [[FMCGUI commands#Structure_menu\|Structure]], and [[~~FMCGUI_commands~~#View_menu\|View]], respectively;		* the bar with six menus: [[FMCGUI commands#Project_Menu\|Project]], [[FMCGUI commands#Data_Menu\|Data]], [[FMCGUI commands#Fragment_menu\|Fragment]], [[FMCGUI commands#Assignment_menu\|Assignment]], [[FMCGUI commands#Structure_menu\|Structure]], and [[FMCGUI commands#View_menu\|View]], respectively;
	*the project main window, where all messages from the last executed command are displayed ;		*the project main window, where all messages from the last executed command are displayed ;
	*the log window, where the history of executed commands is shown.		*the log window, where the history of executed commands is shown.
	<div> </div><div> </div>		<div> </div><div> </div>

AlexLemak at 22:42, 30 November 2009

2009-11-30T22:42:25Z

← Older revision		Revision as of 22:42, 30 November 2009
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	<div></div><div>[[Image:Fmcgui mainwindow.jpg\|thumb\|left\|500px]]</div><div></div><div></div><div></div><div></div><div><br><br><br><br><br><br><br><br><br><br><br><br></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div>The main frame of FMC Graphical Interface consist of 4 sections (see Figure 2.1)<br></div>		<div></div><div>[[Image:Fmcgui mainwindow.jpg\|thumb\|left\|500px]]</div><div></div><div></div><div></div><div></div><div><br><br><br><br><br><br><br><br><br><br><br><br></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div></div><div>The main frame of FMC Graphical Interface consist of 4 sections (see Figure 2.1)<br></div>
	* the title bar displays the name of the current project and the directory inside which the project is located;		* the title bar displays the name of the current project and the directory inside which the project is located;
	* the bar with six menus: [[~~FMCGUI_commands~~#Project_Menu\|Project]], [[~~FMCGUI_commands~~#Data_Menu\|Data]], [[~~FMCGUI_commands~~#~~Fragment_Menu~~\|Fragment]], [[~~FMCGUI_commands~~#~~Assignment_Menu~~\|Assignment]], [[~~FMCGUI_commands~~#~~Structure_Menu~~\|Structure]], and [[FMCGUI_commands#~~View_Menu~~\|View]], respectively;		* the bar with six menus: [[FMCGUI commands#Project_Menu\|Project]], [[FMCGUI commands#Data_Menu\|Data]], [[FMCGUI commands#Fragment_menu\|Fragment]], [[FMCGUI commands#Assignment_menu\|Assignment]], [[FMCGUI commands#Structure_menu\|Structure]], and [[FMCGUI_commands#View_menu\|View]], respectively;
	*the project main window, where all messages from the last executed command are displayed ;		*the project main window, where all messages from the last executed command are displayed ;
	*the log window, where the history of executed commands is shown.		*the log window, where the history of executed commands is shown.
	<div> </div><div> </div>		<div> </div><div> </div>