Sculpting protein conformations: Difference between revisions
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==Samson== | ==Samson== | ||
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>. | 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 set anchor points (shown as gold balls) that remain fixed during dragging. Twister alone does not prevent atomic clashes. To do that, add hydrogens (click '''+H''' in the ''Quick Access'' bar) and turn on '''''Minimize''''' (in the Home tab), which applies a ''universal force field''. After changing the conformation, turn off Twister (press Esc) to release the anchor points, and atom positions will be adjusted automatically to remove any clashes. | ||
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* Interpolation methods are published<ref name="arap1" /><ref name="transition-paths" /><ref name="low-energy-paths" />. | * Interpolation methods are published<ref name="arap1" /><ref name="transition-paths" /><ref name="low-energy-paths" />. | ||
| width="600" |<qt>file=1al1-sculpting-samson-v5-600px.mp4|width=600|height=307|autoplay=false|controller=true|loop=false</qt> | | width="600" |<qt>file=1al1-sculpting-samson-v5-600px.mp4|width=600|height=307|autoplay=false|controller=true|loop=false</qt> | ||
Sculpting [[1al1|1AL1]] with Samson (screen capture}. An anchor point (gold ball) was set at left before the movie starts. Mid-way, an anchor point was set in the middle of the polypeptide. [https://s3.us-east-2.amazonaws.com/molviz.org/downloads/Samson/1al1-sculpting-samson-v5.mp4 Higher resolution version]. | Sculpting [[1al1|1AL1]] with Samson (screen capture}. An anchor point (gold ball) was set at left before the movie starts. Mid-way, an anchor point was set in the middle of the polypeptide. [https://s3.us-east-2.amazonaws.com/molviz.org/downloads/Samson/1al1-sculpting-samson-v5.mp4 Higher resolution version]. ''Minimize'' was not turned on in this movie. | ||
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