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Density Plot

Calculates volumetric gaussian cube files from user supplied structures. These files can be subsequently rendered in VMD and Pymol.


The Density Plot module is accessible from the Analyze section of the main menu.

Basic Usage

The purpose of the module is generate files with volumetric data to visualize results. Often, this is used to visualize sub-ensembles of structures that are in agreement with experimental data.


Screen Shots and Description of Input Fields

This example creates gaussian cube files sample configurations of the HIV-1 Gag protein generated in the Monomer Monte Carlo "constraints" example. The cartoon of the starting structure highlights the flexible regions (red) and structure alignment region (blue) used in the simulation.

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Note that the constraints used in the example allowed the acceptance of trial configurations so that only structures with the center of mass of atoms in residues 240 to 260 were within 40.0 angstroms of the center of mass of CA atoms in residues 400 to 420 were valid.

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Example Output

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The output will indicate the list of files that were written to disk.

Results are written to a new directory within the given "run name" as noted in the output.

Several files are generated and saved to the "run name" density_plot directory.





Output file naming

The general recipe is:

"output file name prefix_"grid spacing"_"weight file flag"_segment_"segment number"_region_"region number".cube

In this example:

output file name prefix : test
grid spacing: 5.0
equal weight file not used:equal_weights
1 segment in molecule: 1
2 regions in segment: region_1 region_2

Region_1 : 240-260
Region_2 : 400-420

This allows one to experiment with different conditions and keep similar files organized.


In the figure below the envelope sampled by all accepted structures is shown along with smaller envelopes described below. The envelopes were visualized using VMD. Three envelopes are displayed in the figure. The blue mesh represents all atoms for each frame of the trajectory, the red mesh represents only CA atoms in region 1 (resid 240-260), and the solid purple mesh represents only CA atoms in regions 2 (resid 400-420).

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A step by step guide to create this figure using VMD is found in the VMD visualization of gaussian cube files: Example 1 page.

Files Used and Created in Example


Module creates output files that are visualized using other program(s) as there are no visualization options built into sassie-web.

Reference(s) and Citations

  1. VMD - Visual Molecular Dynamics W. Humphrey, A. Dalke, K. J. Schulten, Molec. Graphics, 14, 33-38 (1996). BIBTeX, EndNote, Plain Text

  2. SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints J. E. Curtis, S. Raghunandan, H. Nanda, S. Krueger, Comp. Phys. Comm. 183, 382-389 (2012). BIBTeX, EndNote, Plain Text

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