FMAPIq Pipeline - User Help

Session Management

At the top of the interface:

• Show session management: Check to reveal session loading options
• Current Session ID: Displays your active session (auto-created if not specified)
• Uptime: Shows application uptime in days
• Client ID: Unique identifier for occupy system; edit to reclaim access
• Occupy button: Click to occupy/release the system (1-hour automatic timeout)

Loading Sessions

• Load Existing Session ID: Enter or select a session ID to load
• Load from Archive: Upload a .tgz or .tar.gz archive file
• Example session: Use session ID “example” to create a copy of example data

Stage 1: Energy Table

Generates energy table from a PQR file with partial charges.

Input

• PQR File: Upload your protein structure file with partial charges
• Ion Strength (M): Ionic strength in molar (default: 0.016)
• Temperature (C): Temperature in Celsius (default: 25)
• nrot: Number of rotations - 72, 576, or 4608 (default: 72)
• escl: Energy scaling factor (default: 1.0)
• vscl: Nonpolar scaling factor; use negative for automatic calculation based on molecular weight
• Threads: Number of CPU threads to use
• Update Only: Check to reload existing Stage 1 results without recomputing

Output

Displays execution results including molecular weight, number of atoms, and completion status.

Stage 2: Simulation

Runs Monte Carlo simulations to generate protein configurations.

Concentration Options

• Number of proteins: Number of protein molecules in the simulation box
• Box Size (Å): Simulation box dimension in Angstroms

Calculated values (displayed automatically): - Molecular Weight (Da) - Concentration (mg/mL) - Concentration (mM)

Simulation Options

• Replicates: Number of independent replicate simulations (default: 3)
• Cycles: Number of Monte Carlo cycles per replicate (default: 20000)
• Threads per Job: CPU threads allocated to each parallel job
• Parallel Jobs: Automatically calculated (Total threads / Threads per Job)
• Update Only: Check to reload existing Stage 2 results without recomputing

Output

Displays simulation progress and number of configurations generated.

Stage 3: I(q) Calculation

Calculates scattering intensity curves from simulation configurations.

Input

• Box Size (Å): Same as Stage 2
• Spacing: Grid spacing for scattering calculation (default: 1.0)
• Threads: Number of CPU threads to use
• Update Only: Check to reload existing Stage 3 results without recomputing

Output

Displays number of I(q) curves calculated and processing time.

I(q) Plot

Visualizes scattering intensity curves with custom options.

Plot Options

• Show individual curves: Display all replicate curves (not just mean/std)
• Show P(q) reference: Include P(q) form factor reference line
• Log scale (x-axis): Use logarithmic scale for q-axis
• Log scale (y-axis): Use logarithmic scale for intensity axis
• Q min / Q max: Set q-range for plot
• Y min / Y max: Set intensity range for plot

Output

Generates and displays the I(q) plot image.

Download

Direct File Downloads

• Iqs.stat.txt: Statistics file with mean and standard deviation
• Iqs.txt: Full I(q) data for all replicates

Pack Work Directory

Creates a compressed archive of your work directory.

• Skip energy table: Exclude energy table files to reduce archive size
• Skip raw data: Exclude raw simulation data to reduce archive size
• Pack Work Directory: Generate downloadable .tgz archive

Cleanup

Manages session directories to free disk space.

Options

• Days threshold: Remove directories older than this many days (range: 7-365)
• Calculate Size: Preview which directories will be removed and total size
• Cleanup: Permanently delete old directories

Note: The ‘example’ directory is always excluded from cleanup.

Tips

1. Update Only checkbox: Use this to reload results from a previous session without rerunning computations
2. System occupation: When occupied by another user, pipeline stages cannot run
3. Session persistence: Work directories are saved in the sessions/ folder
4. Example data: Load session ID “example” to experiment with pre-computed data