PyMOL Wiki - User contributions [en]

ImmersiveViz

2008-04-19T22:27:13Z

Hazure: /* ImmersiveViz */

==ImmersiveViz==
ImmersiveViz was developed as a component to monitor head tracking and rotate the molecule displayed in such a manner to provide an immersive experience. The ImmersiveViz (MolViz) software integrates two forms of head tracking: Wiimote ''infrared (IR) based'' (active tracking) and ''webcam based'' (passive tracking). By rotating the molecule in a direction opposite to the motion of the user's head we provide a 3D experience; to the user, it appears as if they are 'peeking' around the side of the object. 

Our system contains a head tracking thread which communicates the users position to a PyMol script via a socket. The PyMol script unpacks the message and updates the world respectively. All rotation is done around the virtual origin in PyMol and zoom is also considered. 

We are also developing a Wiimote-based interface whereby the Wii remote can be used as an high degree-of-freedom input device (i.e. a 3d mouse). Comments, questions, and feedback can be sent to [http://groups.google.com/group/molviz molviz (at) googlegroups (dot) com] 

'''Contributed by [http://www.haz.ca/ Christian Muise] and [http://www.cs.toronto.edu/~lilien Ryan Lilien] at the University of Toronto.''' 

== Availability ==

=== Additional Information ===
* '''Project Information:''' http://molviz.cs.toronto.edu/molviz
* '''Project Discussion:''' http://groups.google.com/group/molviz

=== PyMol Script ===
* '''Project Page:''' http://code.google.com/p/immersive-viz/
* '''Source:''' [[http://code.google.com/p/immersive-viz/source/browse/trunk/MolViz.py here]] and [[http://code.google.com/p/immersive-viz/source/browse here]]
* '''Instructions:''' [[http://code.google.com/p/immersive-viz/ here]] and [[http://code.google.com/p/immersive-viz/wiki/UserManual here]]

=== Head Tracking ===
* '''Project Page:''' http://code.google.com/p/htdp/
* '''Source:''' http://code.google.com/p/htdp/source/browse
* '''Instructions:''' http://code.google.com/p/htdp/wiki/Users

[[Category:Script_Library|ImmersiveViz]]

ImmersiveViz

2008-04-19T22:23:30Z

Hazure: /* Additional Information */

==ImmersiveViz==
ImmersiveViz was developed as a component to monitor head tracking and rotate the molecule displayed in such a manner to provide an immersive experience. The ImmersiveViz (MolViz) software integrates two forms of head tracking: Wiimote ''infrared (IR) based'' (active tracking) and ''webcam based'' (passive tracking). By rotating the molecule in a direction opposite to the motion of the user's head we provide a 3D experience; to the user, it appears as if they are 'peeking' around the side of the object. 

Our system contains a head tracking thread which communicates the users position to a PyMol script via a socket. The PyMol script unpacks the message and updates the world respectively. All rotation is done around the virtual origin in PyMol and zoom is also considered. 

We are also developing a Wiimote-based interface whereby the Wii remote can be used as an high degree-of-freedom input device (i.e. a 3d mouse). 

'''Contributed by [http://www.haz.ca/ Christian Muise] and [http://www.cs.toronto.edu/~lilien Ryan Lilien] at the University of Toronto.''' 

== Availability ==

=== Additional Information ===
* '''Project Information:''' http://molviz.cs.toronto.edu/molviz
* '''Project Discussion:''' http://groups.google.com/group/molviz

=== PyMol Script ===
* '''Project Page:''' http://code.google.com/p/immersive-viz/
* '''Source:''' [[http://code.google.com/p/immersive-viz/source/browse/trunk/MolViz.py here]] and [[http://code.google.com/p/immersive-viz/source/browse here]]
* '''Instructions:''' [[http://code.google.com/p/immersive-viz/ here]] and [[http://code.google.com/p/immersive-viz/wiki/UserManual here]]

=== Head Tracking ===
* '''Project Page:''' http://code.google.com/p/htdp/
* '''Source:''' http://code.google.com/p/htdp/source/browse
* '''Instructions:''' http://code.google.com/p/htdp/wiki/Users

[[Category:Script_Library|ImmersiveViz]]

ImmersiveViz

2008-04-15T19:26:16Z

Hazure:

==ImmersiveViz==
ImmersiveViz was developed as a component to monitor head tracking and rotate the molecule displayed in such a manner to provide an immersive experience. The ImmersiveViz (MolViz) software integrates two forms of head tracking: Wiimote ''infrared (IR) based'' (active tracking) and ''webcam based'' (passive tracking). By rotating the molecule in a direction opposite to the motion of the user's head we provide a 3D experience; to the user, it appears as if they are 'peeking' around the side of the object. 

Our system contains a head tracking thread which communicates the users position to a PyMol script via a socket. The PyMol script unpacks the message and updates the world respectively. All rotation is done around the virtual origin in PyMol and zoom is also considered. 

We are also developing a Wiimote-based interface whereby the Wii remote can be used as an high degree-of-freedom input device (i.e. a 3d mouse).

== Availability ==

=== PyMol Script ===
* '''Project Page:''' http://code.google.com/p/immersive-viz/
* '''Source:''' [[http://code.google.com/p/immersive-viz/source/browse/trunk/MolViz.py here]] and [[http://code.google.com/p/immersive-viz/source/browse here]]
* '''Instructions:''' [[http://code.google.com/p/immersive-viz/ here]] and [[http://code.google.com/p/immersive-viz/wiki/UserManual here]]

=== Head Tracking ===
* '''Project Page:''' http://code.google.com/p/htdp/
* '''Source:''' http://code.google.com/p/htdp/source/browse
* '''Instructions:''' http://code.google.com/p/htdp/wiki/Users

For more information, please visit our site [http://molviz.cs.toronto.edu/molviz MolViz]. 

[[Category:Script_Library|ImmersiveViz]]

Ideas

2008-03-12T12:06:48Z

Hazure:

=== PyMOL Ideas Page for Google Summer of Code (GSoC) 2008 and Beyond ===

On behalf of the PyMOL Project, DeLano Scientific LLC has applied for the 2008 Google Summer of Code. Even if we are not chosen, this page should serve as inspiration for ongoing PyMOL development efforts.

== Where to Start ==

Always start with Python and only delve down into the C code when absolutely necessary. Although PyMOL is mostly a C-based application, much of the that code is opaque, fragile, and unforgiving. Although C code refactoring is an important project goal, such work may not be ideal for GSoC-type efforts since once mistake could potentially to destabilize the entire platform.

Fortunately, the Python interpreter and the PyMOL command and selection languages make it possible to extend PyMOL safely and quickly. Even when performance is critical, Python should be the interface between external C, C++, and Java code and PyMOL's internal C data structures.

== Choosing a Topic ==

The best open-source code is usually written by an end-users attempting to meet their own pressing needs. So if you have already have a specific need which relates to PyMOL, then we strongly encourage you to follow up on that first!

If you are looking for ideas, then try to seek out enhancements and/or integrations that will impact the largest potential user base. For example, imagine what new things might be useful to virtually all medicinal chemists, all structural biologists, all movie-makers, all paper-writers, and so forth.

The ideas below are organized by category. Right now, integration with other open-source projects seems like the approach most likely to yield significant benefit, so those ideas are first.

== Integration Ideas (Linking Out to Useful Open-Source Tools) ==

In most cases, depending on the need, integration can be accomplished through standalone Python scripts, through new PyMOL commands, through PyMOL Wizards, or via Tkinter plugins.

* APBS (electrostatics calculations): Improve the existing plugin. Michael Lerner is currently leading this effort. See [[APBS]]
* RDKit (cheminformatics, depiction, UFF cleanup, etc.): Lots of potential here, however C++ coding may be necessary for more advanced integration tasks. [http://www.rdkit.org RDKit home]
* mengine (MMFF small molecule cleanup): work is in progress (Delsci).
* mpeg_encode (MPEG movie production on Linux, etc.): work is in progress (Delsci).
* GIMP (image manipulation): Streamline & document the process of exporting images from PyMOL into GIMP and preparing them for submission to scientific Journals.
* Blender (general-purpose 3D modeling & animation): Streamline & document the process of getting molecular geometry out of PyMOL and into Blender.
* Jmol (publishing visualizations inside of web pages): Liason between PyMOL & Jmol projects to develop a shared molecular visualization data model compatible with both applications.
* Firefox (plugin): Develop an PyMOL plugin compatible with Firefox.
* MMTK (molecular mechanics -- Python/flexible): Develop the ability to round-trip molecular systems from PyMOL, into MMTK, and back.
* GROMACS (molecular mechanics -- C/fast) - Maybe some ideas can be shared with this guy. [http://www.kde-apps.org/content/show.php/Gromacs+GUI+?content=47665 Gromacs GUI]
* OpenOffice (escape Microsoft hegemony): Develop an PyMOL plugin.
* IPython integration (interactive shell): a robust alternative to the PyMOL command line?
* R (statistics): PyMOL a 3D viewer environment for visualizating & manipulating large statistical data sets?

Are there other key open-source packages we might specifically target for integration with PyMOL, either through GSoC or beyond?

== High-Level Enhancement Ideas (Mostly Python-oriented) ==

* Work on [[#More Ideas (Please add your own!)| [MolViz]]]
* Develop new plugins which automate routine tasks.
* Improve the Python API documentation.
* Flesh out the new "from pymol2 import PyMOL" instance-based PyMOL API.
* Develop alternate Tkinter "skins" (for custom OEM-like applications).
* Develop a Tkinter/TOGL widget which holds a PyMOL viewer instance.
* Develop a PyQt widget which holds a PyMOL viewer instance.
* Create a plugin-manager GUI in the style of Firefox, Rythmbox, Gedit, Eclipse. A GUI where it is easy to turn off/on plugins, configure them and see help-contents for them. Maybe also some way to paste a url to install a new Plugin.
* Add a plugin for a GUI window with the same functionality as the "Control Panel" window in SwissPDB Viewer.
* Extend and modify the PyMOL command language so as to be compatible with existing RasMol and/or Jmol scripts.
* Enhance the Mutagenesis Wizard in order to support Nucleic acids and/or Sugars.
* Streamline the process of creating movies out of Scenes.

== Low-Level Enhancement Ideas (Mostly C-oriented) ==

* Provide a "split" view with multiple molecules each in their own pane (already partially implemented).
* Add a movie slider similar to that found in Maya, Cinema4D, 3DSMax.
* Enable editing of displayed sequence alignments.
* Add multi-line textual annotations
* Support additional annotation object including: arrow, lines, and blobs.
* Add display of secondary structure into the sequence viewer.
* Enable per-object Z clipping (especially in the ray tracer)
* Hilite H-bonds, salt bridges, Pi-stacking, Pi-cations, etc.
* Build in a simple forcefield and energy minimizer suitable for use with Mutagenesis.
* Improve the ability to animate objects independently when creating movies.
* Incorporate a suite of standard NMR visualizations (restraint violations, per-residue RMS, etc.)
* Enumeration and display of low-energy conformers.
* Automated structure grafting (poor-man's homology modeling).
* Import of alignment files.

== Difficult C-level Code Refactoring Ideas ==

* Assemble a test suite which thoroughly exercises the existing code (a prerequisite to major refactoring).
* Catch & handle memory-allocation failures gracefully (instead of crashing).
* Replace PyMOL's memory management & custom containers with a simple runtime object model.
* Separate the View and the Controllers from the Model so that they can all run asynchronously (on multiple cores).
* Enable generalized undo of changes made to the Model.
* Clean up the internal matrix handling code.

== Ideas Involving Proprietary APIs ==

Since these involve closed-source APIs and infrastructure, they aren't suitable for GSoC. However, such requests are noted here for the sake of complete coverage. These development projects may be available to independent contractors outside of GSoC.

* Build an ActiveX Control for PowerPoint and/or Internet Explorer (work is in progress - Delsci)
* Support direct export of Windows Media files (AVI movies).
* Create a Windows port with "native" look & feel. <- Could this be done in PyQT or PyGTK?. Then it would look "native", but be cross-platform and not proprietary.
* Integrate directly via Mathematica via MathLink.
* Further enhance JyMOL (Java-JNI/wrapped PyMOL)
* Integrate with Matlab.

== More Ideas (Please add your own!) ==
* [http://molviz.cs.toronto.edu/molviz MolViz] is a project to incorporate head tracking input into [http://pymol.sourceforge.net/ PyMol]. This is accomplished through a [http://www.pymolwiki.org/index.php/ImmersiveViz script] written in Python to control the molecule's position using the existing [http://www.pymolwiki.org/index.php/Category:Commands PyMol API]. Related projects would include:
** Improving the existing [http://www.pymolwiki.org/index.php/ImmersiveViz PyMol plugin] for more precise control of the environment.
** Developing new input drivers for the Wiimote form of control. This would require some bluetooth hacking.
** Implementing some other forms of input for head tracking, such as fisheye head tracking, IR webcam tracking, etc (refer to the end of this [[http://www.youtube.com/watch?v=ncShaY4VSac video]] for a better description).
* Provide a 2D chemical depiction of the current 3D view.
* Spreadsheet view with additional information (e.g. IC50's).
* Create additional documentation, screen casts, & tutorials.
* Export 3D PDF images.

ImmersiveViz

2008-03-10T22:09:17Z

Hazure:

==ImmersiveViz==
ImmersiveViz was developed as a component to monitor head tracking and rotate the molecule displayed in such a manner to provide an immersive experience. The head tracking is done by a number of different forms of input and sent over a socket where ImmersiveViz reads the coordinates and updates the world respectively. All rotation is done around the virtual origin in PyMol and zoom is also considered. 
 
For more information, please visit our site [http://molviz.cs.toronto.edu/molviz MolViz]. Downloads will be available by the end of March '08.

[[Category:Script_Library|ImmersiveViz]]

ImmersiveViz

2008-03-10T22:09:02Z

Hazure: New page: ==ImmersiveViz== EZ-Viz was developed as a component to monitor head tracking and rotate the molecule displayed in such a manner to provide an immersive experience. The head tracking is do...

==ImmersiveViz==
EZ-Viz was developed as a component to monitor head tracking and rotate the molecule displayed in such a manner to provide an immersive experience. The head tracking is done by a number of different forms of input and sent over a socket where ImmersiveViz reads the coordinates and updates the world respectively. All rotation is done around the virtual origin in PyMol and zoom is also considered. 
 
For more information, please visit our site [http://molviz.cs.toronto.edu/molviz MolViz]. Downloads will be available by the end of March '08.

[[Category:Script_Library|ImmersiveViz]]

Category:Script Library

2008-03-10T22:03:57Z

Hazure:

= Overview =
Here we provide a trove of scripts. The descriptions immediately follow. For the entire category, please see the bottom of this page.

= Descriptions =

* [[ImmersiveViz]] -- A script used in conjunction with head tracking software to provide an immersive virtual experience.

* [[Rasmolify]] -- A work in progress - a script to map Rasmol commands onto the equivalent PyMOL commands.

* [[Zero_residues]] -- Renumber residues such that the first residue is 0. Useful for alignments.

* [[Cealign]] -- Implementation of the CE Structure Alignment algorithm as a PyMOL plugin.

* [[WriteSS]] -- Writes secondary structural elements, for each residues, to a file.

* [[Process_All_Files_In_Directory]] -- Do something to all files in a directory. The examples show how to print the disulfide bond lengths, then in general all sulfur distances (not necessarily bound).

* [[Kabsch]] -- Kabsch alignment of two sets of vectors. (Part 2 of a protein alignment.)

* [[Transform_odb]] -- Transform a selection of an existing object and output as a new object. The transformation matrix is read from an "O"-style tranformation matrix file (.odb) written by "O" or by any of the Uppsala Software Factory programs (from Gerard Klegweit) such as LSQMAN.

* [[Stereo_Ray]] -- This script will create two resolution specific ray traced images rotated appropriately for inclusion into a single file to represent a stereo view of the desired macromolecule.

* [[Translate_And_Measure]] -- prints '''overlap''' if any of the atoms in molA or molB were within 4 Angstrom after translating by 1 along X

* [[Show aromatics]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for aromatic residues displayed as green "sticks". Usage: Save this as "show_aromatics.pml", load your protein in PyMOL, and run the script (select "Run" from the "File" menu). (PyMOL script; TStout)

* [[Show hydrophobics]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophobic residues displayed as orange "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show charged]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for charged residues displayed as red (negative) or blue (posititve) "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show hydrophilic]] -- This script will display a backbone "worm" for your protein, with all of the sidechains for hydrophilic residues displayed as green "sticks". Usage: Same as "show aromatics". (PyMOL script; TStout)

* [[Show NMR constrains]] -- This script will display the NMR constrains used for a structure calculation atop a structure. Usage: Save this as "NMRcnstr.py" load your protein in PyMOL, and run the script. type upl('fname') or cns('fname') where fname is the filename with the NMR constrains you want to display.

* [[Perp Maker]] -- Creates a perpendicular plane through the center of your protein with respect to the camera's current position. (If you translate the protein towards the camera a bit, you get a nice surface, sometimes.) A stupid little script I wrote in response to a request a few months ago (and it doesn't even conform to the request!) Load a protein, run the script (read the documentation in the script). (Jason Vertrees/[[User:Tree|Tree]])

* [[PythonTerminal]] -- Allows execution of python commands from the PyMOL command line.

* [[Axes]] -- Creates a 3D-CGO object that shows the three coordinate axes.

* [[Symmetry Axis]] -- Draw a 3D-CGO line given a point and a direction.

* [[CGO Text]] -- Creates a 3D-CGO text object.

* [[List Selection]] -- Prints a list of all residues in a selection (both Python and .pml).

* [[List Colors]] -- Lists the color of all residues in a selection (both Python and .pml).

* [[List Secondary Structures]] -- Secondary structures (both predefined and those calculated with the 'dss' command) can be exported as a long string ('HHHHLLLLSSS').

* [[Split Movement]] -- Moves two parts of one object into different directions.

* [[Selection Exists]] -- Python method that returns true if a selection of a given name exists.

* [[Get Coordinates I]] -- Retrieves atom coordinates as Python objects.

* [[Get Coordinates II]] -- Retrieves atom coordinates as Python array (list object).

* [[grepset]] -- List all settings matching a given keyword. - ''by EHP''

* [[apropos]] -- List all commands matching a given keyword or whose docs contain the keyword. - ''by EHP''

* [[mouse_modes]] -- customize the default mouse bindings for Viewing or Editing modes. - ''by EHP''

* [[Measure Distance]] -- Measures the distance between two atoms (Python script).

* [[Read PDB-String]] -- Parses a string in PDB format to a PyMOL object.

* [[Color Objects]] -- Colors all objects differently (Python script).

* [[Key Wait]] -- Process key events in a Python script.

* [[Bounding Box]] -- Create a bounding box around a selection (Python script; requires numarray and Scientific; gilleain)

* [[Ellipsoid]] -- Create callback object (opengl) ellipsoids. (Python script; gilleain)

* [[pdbsurvey]] -- Surveys the pdb for recently added structures that are relevant to a user-specified keywords list (in a text file)

* [[resicolor]] -- Colors proteins according to residue type.

* [[TransformSelectionByCameraView]] -- Transforms the selection by the camera view.

* [[WFMesh]] -- Imports wavefront object mesh files; Starwars as an example!

* [[grepsel]] -- Make named selections using regular expressions (protein sequence).

* [[PowerMate Dial OS X]] -- Script and instructions to use the PowerMate dial on Mac OS X.

* [[Plane Wizard]] -- Wizard to draw planes between three picked points.

* [[Slerpy]] -- Pymol command extensions for key frame animation movie making.

* [[Helicity_check]] -- helicity_check show the evolution of O - N distances over an amino acid sequence

* [[Center Of Mass]] -- Given a selection of atoms (of equal weight) - Calculates the center of mass and represents it with a CGO sphere

* [[ss]] -- Simple command to summarise the Secondary Structure as a list of "start-end type" like sses.

* [[iterate_sses]] -- Slightly more complex version of "ss" that allows the user to pass in a function to act on the sse list.

* [[motif]] -- Designed for easy display of backbone motifs (nests, catgrips, etc).

[[Category:Scripting|Script Library]]