Overview
The Run MMC tab is used to perform Monomer Monte Carlo (MMC) simulations to explore possible conformational flexibility in the structural model. This simulation generates a series of structural variations, helping to refine the fit between experimental and computational data for both I(q) and P(r).
Fields in the Run MMC Tab
Below the standard Project Name and Description fields, the MMC tab contains the following fields:
- Downloads: Allows downloading the starting structure in "PDB" or "mmCIF" formats, and the experimental "Iq" and "Pr" files. Right-click on these labels to access the download options.
- Run Name: Automatically generated by appending the project name to "run" (not editable).
- Reference PDB: Reports the starting structure filename for the MMC run (not editable).
- Output File Name (DCD): Generated by appending ".dcd" to the run name. Contains all the structures sequentially generated in the MMC run (not editable).
- Number of Trial Attempts: Total number of sequential steps in the MMC run (default: 50,000). User modifiable. For this example, 20,000 steps were used.
- Return to Previous Structure: Set to "20". After this number of failed steps, the program resets to the current coordinates (not user modifiable).
- Temperature (K): Fixed at 300 K (not user modifiable).
- Molecule Type: Set to "protein" (not user modifiable).
- Number of Flexible Regions to Vary: Defined in the previous tab, not user modifiable here.
- Residue Range for Each Flexible Region: Defined in the previous tab, not user modifiable here.
- Maximum Angle(s): Set to 30°, which is the maximum torsion angle each flexible region can sample in a single move (not user modifiable).
- Structure Alignment Range: Residue range used to spatially align all MMC-generated models. Should correspond to a non-flexible region. User modifiable.
- Overlap Basis: Defines the basis for overlap checks to reject structures with clashes. Default is "heavy atoms." Other options include:
- "all" atoms (if H atoms are defined).
- "backbone" atoms.
- Manually entered atom name.
Steps to Run MMC
- Configure the Input: Review the fields above and modify user-modifiable parameters as needed, such as Number of Trial Attempts and Structure Alignment Range.
- Run the MMC Simulation: Press Submit to launch the MMC run. A progress bar and percentage updates will display the simulation status.
Outputs and Visualization
Once the MMC run is completed:
- A graph displaying the radius of gyration (Rg) for all generated and accepted structures as a function of structure number will be shown.
- A printed summary will include the number of accepted structures over the total generated.
- Other key metrics and details from the run will be reported for further analysis.