Resonance Assignment/Abacus/FMCGUI objects

 

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 {[[FMCGUI commands#Data&gtN15 NOESY>|Data>”Peak list name”>Load] or {Project>Load} commands.

For some peak-lists, peaks in the list should be referenced by spin-system (fragment) user ID.

The following table shows referencing requiments for different peak lists.

Here:

• (+)    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 {[[FMCGUI commands#Fragment>Load]]}, {FMCGUI commands#Fragment>Create>abacus}, or {FMCGUI commands#Project>Eload} 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, that indicate 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 commands[Assignment>Fix Assignment>Manually], [Assignment>Fix Assignment>Using probability Map], and [Assignment>Fix Assignment>Reset all].

Typing probabilities

    Typing probabilities    , where t correspond to one of 20 amino acid residue types.is a probability for fragment U_id to have a type t. It could be calculated or modified by the commands [Fragment>Type>Calculate] and [Fragment>Type>Fix].

Contact map

    Each fragment has three Fragment contact maps: ,  , and , respectively. Each contact map scores the possibility for any fragment f to be next to fragment U_id in the protein sequence; were f and U_id stand for fragment user ID.

is calculated from HNCA spectrum by the command   [Assignment>Contact>HNCA]

 Fragment   contact maps  and , calculated from NOESY spectra with and without using BACUS procedure, respectively;

    can be calculated by the commands   [Assignment>Contact>NOE>fawn]    and [Assignment>Contact>NOE>abacus], while  is calculated by [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.