Resonance Assignment/Abacus/FMCGUI objects: Difference between revisions
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=== Contact map === | === Contact map === | ||
:There are three fragment contact maps: C<sup>f1</sup><sub>CA | :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 | <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 {Assignment>Contact>HNCA}</span></div><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 {Assignment>Contact>NOE>fawn} and {Assignment>Contact>NOE>abacus}, while </span>C<sup>f1</sup><sub>B</sub><span>(f2) </span><span /><span> is calculated by command {Assignment>Contact>NOE>abacus}.</span></div><div> </div> | ||
=== Assignment probabilities === | === Assignment probabilities === | ||
Revision as of 21:43, 30 November 2009
Most of FMCGUI commands operate mainly with the following three objects that are located in computer memory:
- protein sequence
- peak list
- and PB fragments.
Protein sequence
This object can be created in memory using {Data>Protein Sequence>Load } or {Project>Load} commands.
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.
Peak list
Different peak lists objects can be created in memory using {Data>”Peak list name”>Load} or {Project>Load
- (+) peak list is required to be referenced
- (+/-) peak lists could be referenced optionally
- (-) peak lists for which referencing is not used even if it is present in the input file
N15 NOESY
|
-
|
C13 NOESY H2O
|
-
|
Arom NOESY
|
-
|
N15 HSQC
|
+
|
C13 HSQC
|
+
|
HNCA
|
+/-
|
HNCO
|
-
|
CBCACONH
|
+/-
|
HBHACONH
|
+
|
List of PB fragments
This object can be created in memory using {Fragment>Load>}, {Fragment>Create>abacus}, or {Project>Load} commands.
Each PB fragment in the list has the following main properties:
User ID
Fragment ID assigned by user, U_id. U_id can’t be changed within FMCGUI.
Assignment ID
Assignment ID, A_id, indicates the sequence position ID to which the fragment is assigned.
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 {Assignment>Fix Assignment>Manually}, {Assignment>Fix Assignment>Using probability Map}, and {Assignment>Fix Assignment>Reset all }.
Typing probabilities
Tt (f) is a probability for fragment f to have amino acid type t. Here t corresponds to one of 20 amino acid residue types, and f is fragment user ID.
Typing probbilities could be calculated or modified manually by the commands {Fragment>Type>Calculate} and {Fragment>Type>Fix}, respectively.
Contact map
- There are three fragment contact maps: Cf1CA(f2) , Cf1B(f2) , and Cf1F(f2) , respectively. Each contact map scores the possibility for any fragment f1 to be next to the fragment f1 in protein sequence. Here f1 and f2 stand for fragment's user ID.
Fragment contact map Cf1CA(f2) is calculated based on HNCA spectrum by the command {Assignment>Contact>HNCA}
Fragment contact maps Cf1B(f2) and Cf1F(f2) <span /> are calculated from NOESY spectra with or without using BACUS procedure, respectively.
Cf1F(f2) can be calculated for all values of f1 and f2 by both commands {Assignment>Contact>NOE>fawn} and {Assignment>Contact>NOE>abacus}, while Cf1B(f2) is calculated by command {Assignment>Contact>NOE>abacus}.
Assignment probabilities
- FragmentFragment assignment probabilities and are calculated using SA and REM Monte Carlo simulations, respectively. Here s stands for protein sequence position ID.
is calculated by command [Assignment>Calculate probabilities>SA] or it can be loaded in memory using command [Assignment>Load probabilities];
is calculated by command [Assignment>Calculate probabilities>REM] or it can be loaded in memory using command [Assignment>Load probabilities];
The current values of all these properties for a particular fragment could be observed in the “Fragment Graph “window which is opened by command [View>Fragment]
Main window
The main frame of FMC Graphical Interface consist of 4 sections (see Figure 2.1)
- the title bar displays the name of the current project and the directory where the project is located;
- the bar with six menu: Project, Data, Fragment, Assignment, Structure, and View, respectively;
- the main message window, where message from the last executed command is displayed ;
- the log window, where the history of executed commands is shown.