Visualization
For the visualization and modeling of volumetric maps in concert with docked structures we recommend the free graphics programs VMD, Chimera or Sculptor, which support map formats used by Situs. Any graphics program that can render structures in PDB format together with 3D density maps is suitable for Situs. Historically, VMD was used for the Situs tutorials - and is still widely featured in this web documentation - but we will point to advantages of Chimera or Sculptor as is appropriate.

In addition to these graphics programs, Situs also provides analysis and rendering capabilities in the terminal window. The following figure shows three typical analysis and graphics utilities used in the Situs workflow:


(Click image to enlarge)



(Left:) Molecular rendering of biomolecular structures and volumes (using VMD). (Right:) Analysis of the voxel histogram with volhist, and display of volumetric data cross sections during data editing with voledit.
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