Sculpting protein conformations
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This page is under development starting February 29, 2020. Please come back later to see it more fully developed. |
Planned contents include PyMOL, Samson, and (now defunct) Sculpt. These programs enable protein conformations to be "sculpted" by dragging with the mouse.
Sometimes it is instructive to change the conformation of a protein model. Typically this means "sculpting" an experimentally-determined (empirical) model into a hypothetical conformation with some functional significance. There are software packages that enable this to be done manually, using the mouse to drag portions of the original model into desired conformations.
As you sculpt a protein model, you are morphing it into a new conformation. However, molecular morphing usually means making a movie or animation that shows interpolated transitioning between two conformations, which may be empirical or theoretical. There are many examples of molecular morphs in Proteopedia.
SamsonSamson
The free, open-source program Samson is available from samson-connect.net and in 2020 is under active development by OneAngstrom.Com. Samson has an extension application named Twister that enables dragging portions of a protein into new conformations with the mouse.
Pros
- Anchor points can be set that remain fixed during sculpting.
- Minimization occurs in real time during dragging.
- Free software.
Cons
- Atomic clashes and unrealistic bond distances and angles may occur.
Related ResourcesRelated Resources
- Sculpt[1], a program initially released in 1994 by Mark Surles, Jane Richardson, David Richardson, and Frederick P. Brooks, Jr., is described with the theoretical structure 1ssr.
- User:Wayne Decatur/Generate Unfolded Structures
- User:Wayne Decatur/Molecular modeling tools
- Molecular modeling and visualization software