Sculpting protein conformations: Difference between revisions
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The free, open-source program Samson is available from [http://samson-connect.net samson-connect.net] and in February 2020 is under active development by [http://oneangstrom.com OneAngstrom.Com]: see [https://documentation.samson-connect.net/whats-new-in-samson-2020-the-open-molecular-modeling-platform/ What's New in Samson 2020?]. Samson has an extension application named '''''Twister''''' that enables dragging portions of a protein into new conformations with the mouse. Real-time minimization occurs while dragging, following the ''as-rigid-as-possible'' interpolation path<ref name="arap1">PMID:28321532</ref><ref name="low-energy-paths">PMID: 30069648</ref>. You can click on atoms to set anchor points (shown as gold balls) that remain fixed during dragging. A video showing how to do this, step by step, is available at [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins]. | The free, open-source program Samson is available from [http://samson-connect.net samson-connect.net] and in February 2020 is under active development by [http://oneangstrom.com OneAngstrom.Com]: see [https://documentation.samson-connect.net/whats-new-in-samson-2020-the-open-molecular-modeling-platform/ What's New in Samson 2020?]. Samson has an extension application named '''''Twister''''' that enables dragging portions of a protein into new conformations with the mouse. Real-time minimization occurs while dragging, following the ''as-rigid-as-possible'' interpolation path<ref name="arap1">PMID:28321532</ref><ref name="low-energy-paths">PMID: 30069648</ref>. You can click on atoms to set anchor points (shown as gold balls) that remain fixed during dragging. A video showing how to do this, step by step, is available at [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins]. | ||
Twister alone does not prevent atomic clashes | Twister alone does not prevent atomic clashes, but they can be avoided by turning on '''''Minimize''''', which applies a ''universal force field''. This is demonstrated in the movie available at [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins]. Samson can also create simulations that use any of a number of force fields provided, such as GROMACS (not illustrated here -- see [https://documentation.samson-connect.net/simulating-small-molecules-graphene-and-proteins/ Simulating small molecules and proteins]). | ||
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