Resonance Assignment/Abacus/FMCGUI objects

 

Most of FMCGUI commands operate mainly with the following three objects that are loaded into computer memory: 

• protein sequence
• peak list
• PB fragments

 

Protein sequence

The protein sequence can be loaded into the program using {Data>Protein Sequence>Load } or {Project>Load} commands.

The position ID of the first residue in the sequence should be specified by the user when loading the sequence file (when it is not specified in the input file). Some commands in FMCGUI assume that the first residue of the protein sequence has position ID of 1. Therefore, if there is a HIS-tag, the loaded sequence should be numbered accordingly with a negative position ID for the first residue.

 

Peak list

Different peak lists can be loaded into the program using {Data>”Peak list name”>Load} or {Project>Load}

• (+)    peak list needs to be referenced
• (+/-)  peak lists could be referenced, but it isn't necessary
• (-)     peak lists could be referenced, but it won't be used by FMCGUI
                               

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

     T^t (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 can be calculated or modified manually by the commands {Fragment>Type>Calculate} and  {Fragment>Type>Fix}, respectively.

Contact map

There are three fragment contact maps: C^f1_HNCA(f2)  , C^f1_{NOE_B}(f2) ,  and C^f1_{NOE_F}(f2) , respectively. Each contact map scores the possibility for any fragment f1 to be next to the fragment f2 in protein sequence. Here f1 and f2 stand for fragment's user ID.

 Fragment contact map  C^f1_HNCA(f2) is calculated based on HNCA spectrum by the command   {Assignment>Contacts>HNCA}

 Fragment   contact maps C^f1_{NOE_B}(f2)   and C^f1_{NOE_F}(f2)   are calculated from NOESY spectra with or without using BACUS procedure, respectively.

   C^f1_{NOE_F}(f2)   can be calculated for all values of f1 and f2 by both commands   {Assignment>Contacts>NOE>fawn}   and {Assignment>Contact>NOE>abacus}, while   C^f1_{NOE_B}(f2)  is calculated by  command {Assignment>Contact>NOE>abacus}.

 

Assignment probabilities

  

P^s(f) is a probability of fragment f to be assigned to sequense position s, where f is fragment user ID, and s is sequence position ID. There are two assignment probabilities associated with a fragment - P^s_SA(f) and P^s_REM(f) - that are calculated using Simulates Annealing (SA) and Replica Exchange Method (REM) Monte Carlo simulations, respistively.

 P^s_SA(f)    is calclated by command {Assignment>Calculate Probabilities>SA} 

 P^s_REM(f)  is calculated by command {Assignment>Calculate probabilities>REM}.

Both assignment probabilities could be also  loaded in memory from already performed calculations using command {Assignment>Load probabilities}.

 

Main window

Figure 2.1

The main frame of FMC Graphical Interface consist of 4 sections (see Figure)

•  the title bar displays the name of the current project and the directory inside which the project is located;
•  the bar with six menus: Project, Data, Fragment, Assignment, Structure, and View, respectively;
• 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.