Sculpting protein conformations: Difference between revisions
Eric Martz (talk | contribs) No edit summary |
Eric Martz (talk | contribs) |
||
| (10 intermediate revisions by the same user not shown) | |||
| Line 20: | Line 20: | ||
* No official documentation for using ''Twister'' from the ''Samson'' team in March, 2020, but see the step by step video at [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins]. | * No official documentation for using ''Twister'' from the ''Samson'' team in March, 2020, but see the step by step video at [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins]. | ||
| 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]. ''Minimize'' was not turned on in this movie. | Sculpting [[1al1|1AL1]] with Twister in 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. | ||
|} | |} | ||
| Line 34: | Line 34: | ||
* Minimization occurs in real time during dragging. | * Minimization occurs in real time during dragging. | ||
'''Cons''' | '''Cons''' | ||
* Sculpting in PyMOL is described as unsupported (see below) and there is no detailed documentation. However see the step-by-step instructional movie at [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins]. | |||
* PyMOL is not free, although many institutions have site licenses, and you may be able to obtain a free version for educational uses. | * PyMOL is not free, although many institutions have site licenses, and you may be able to obtain a free version for educational uses. | ||
| width="600" |<qt>file=1al1-stretch-pymol.mp4|width=615|height=260|autoplay=false|controller=true|loop=false</qt> | | width="600" |<qt>file=1al1-stretch-pymol.mp4|width=615|height=260|autoplay=false|controller=true|loop=false</qt> | ||
Sculpting [[1al1|1AL1]] with PyMOL (screen capture}. A video showing how to do this, step by step, is available at [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins]. | Sculpting [[1al1|1AL1]] with PyMOL (screen capture}. A video showing how to do this, step by step, is available at [http://tinyurl.com/sculpting-proteins tinyurl.com/sculpting-proteins]. | ||
|} | |} | ||
* [https://www.youtube.com/watch?v=d5SP28Gt-7Y Using PyMOL sculpting to tighten/untie a trefoil knot] is a useful video on YouTube. | |||
* [https://pymolwiki.org/index.php/Molecular_Sculpting Molecular Sculpting] in the PyMOL wiki, a brief set of instructions written by [[User:Warren DeLano|Warren DeLano]]. | |||
* [https://pymol.org/dokuwiki/doku.php?id=sculpting sculpting] at pymol.org lists a few commands. | |||
*[https://pymol.org/dokuwiki/doku.php?id=setting:sculpt setting:sculpt] at pymol.org lists many commands. | |||
*[https://pymolwiki.org/index.php/Modeling_and_Editing_Structures Modeling and Editing Structures] at pymolwiki.org explains command-based methods for sculpting in PyMOL. | |||
==Sculpt (defunct)== | ==Sculpt (defunct)== | ||
Sculpt<ref name="sculpt" /> is no longer available. It was initially released in 1994 by Mark Surles, [[User:Jane S. Richardson|Jane Richardson]], David Richardson, and Frederick P. Brooks, Jr., and is described with the theoretical structure [[1ssr]]. Formerly it was available as a stand-alone program, and also it was built-into [[Chime]]. A simulation of inhibitor binding to HIV protease that was created with Sculpt can be viewed at [[Molecular Playground/HIV Protease Inhibitor]]. | Sculpt<ref name="sculpt" /> is no longer available. It was initially released in 1994 by Mark Surles, [[User:Jane S. Richardson|Jane Richardson]], David Richardson, and Frederick P. Brooks, Jr., and is described with the theoretical structure [[1ssr]]. Formerly it was available as a stand-alone program, and also it was built-into [[Chime]]. A simulation of inhibitor binding to HIV protease that was created with Sculpt can be viewed at [[Molecular Playground/HIV Protease Inhibitor]]. A simulation of water molecules coalescing into a nano-droplet was done with Sculpt, and can be found at [http://molviz.org MolviZ.Org] or by going directly to [http://biomodel.uah.es/en/water/p2.htm Water at BioModel]. | ||
==Related Resources== | ==Related Resources== | ||
* ''Sculpt''<ref name="sculpt">PMID:8003957</ref>, a program initially released in 1994 by Mark Surles, Jane Richardson, David Richardson, and Frederick P. Brooks, Jr. | * [[1ssr|1SSR]], a theoretical structure, is accompanied by a publication describing ''Sculpt''<ref name="sculpt">PMID:8003957</ref>, a program initially released in 1994 by Mark Surles, Jane Richardson, David Richardson, and Frederick P. Brooks, Jr.. | ||
*[[User:Wayne Decatur/Generate Unfolded Structures]] | *[[User:Wayne Decatur/Generate Unfolded Structures]] | ||
*[[User:Wayne Decatur/Molecular modeling tools]] | *[[User:Wayne Decatur/Molecular modeling tools]] | ||
*[[Molecular modeling and visualization software]] | *[[Molecular modeling and visualization software]] | ||
* See the list of links above under PyMOL. | |||
==References== | ==References== | ||
<references /> | <references /> | ||