PyMOL: Difference between revisions

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[http://pymol.org PyMOL] is a stand-alone [[Molecular modeling and visualization software|molecular visualization]] program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren DeLano]. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.

Molecular scenes prepared in PyMOL can be imported into Protoepedia scenes. [[Jmol]] which Proteopedia, uses for displaying molecular scenes can read a PyMOL session files (.pse file) that you have saved on your computer and convert it directly into a Jmol scene to be saved and displayed in Proteopedia. Specifically, if you open Proteopedia's Scene Authoring Tool, you can click-and-drag the PyMol session file from your computer's file browser interface into the structure window of the Scene Authoring Tool (on the right). Jmol will then make its best attempt at reproducing the scene. You can then use the Scene Authoring Tool interface to save that scene to Proteopedia in [[Scene authoring tools#~~.27save_scene.27_tab~~ the typical way]].

Molecular scenes prepared in PyMOL can be imported into Protoepedia scenes. [[Jmol]] which Proteopedia, uses for displaying molecular scenes can read a PyMOL session files (.pse file) that you have saved on your computer and convert it directly into a Jmol scene to be saved and displayed in Proteopedia. Specifically, if you open Proteopedia's Scene Authoring Tool, you can click-and-drag the PyMol session file from your computer's file browser interface into the structure window of the Scene Authoring Tool (on the right). Jmol will then make its best attempt at reproducing the scene. You can then use the Scene Authoring Tool interface to save that scene to Proteopedia in [[Scene authoring tools#'save_scene'_tab the typical way]].

PyMOL has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a current [http://pymol.org/educational.html free version] is available to students and educators for classroom use, old out-of-date binary builds can be [http://delsci.com/rel/099 freely downloaded] by anyone, and some Linux distributions provide [http://packages.debian.org/stable/pymol PyMOL packages] compiled from the open-source code.

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 [http://pymol.org PyMOL] is a  stand-alone [[Molecular modeling and visualization software|molecular visualization]] program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of [http://www.delanoscientific.com/ Warren DeLano].  Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.
-Molecular scenes prepared in PyMOL can be imported into Protoepedia scenes. [[Jmol]] which Proteopedia, uses for displaying molecular scenes can read a PyMOL session files (.pse file) that you have saved on your computer and convert it directly into a Jmol scene to be saved and displayed in Proteopedia. Specifically, if you open Proteopedia's Scene Authoring Tool, you can click-and-drag the PyMol session file from your computer's file browser interface into the structure window of the Scene Authoring Tool (on the right). Jmol will then make its best attempt at reproducing the scene. You can then use the Scene Authoring Tool interface to save that scene to Proteopedia in [[Scene authoring tools#.27save_scene.27_tab the typical way]].
+Molecular scenes prepared in PyMOL can be imported into Protoepedia scenes. [[Jmol]] which Proteopedia, uses for displaying molecular scenes can read a PyMOL session files (.pse file) that you have saved on your computer and convert it directly into a Jmol scene to be saved and displayed in Proteopedia. Specifically, if you open Proteopedia's Scene Authoring Tool, you can click-and-drag the PyMol session file from your computer's file browser interface into the structure window of the Scene Authoring Tool (on the right). Jmol will then make its best attempt at reproducing the scene. You can then use the Scene Authoring Tool interface to save that scene to Proteopedia in [[Scene authoring tools#'save_scene'_tab the typical way]].
 PyMOL has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a current [http://pymol.org/educational.html free version] is available to students and educators for classroom use, old out-of-date binary builds can be [http://delsci.com/rel/099 freely downloaded] by anyone, and some Linux distributions provide [http://packages.debian.org/stable/pymol PyMOL packages] compiled from the open-source code.