https://wiki.pymol.org/api.php?action=feedcontributions&user=Martoss&feedformat=atomPyMOL Wiki - User contributions [en]2024-03-28T15:48:00ZUser contributionsMediaWiki 1.35.1https://wiki.pymol.org/index.php?title=Grid_slot&diff=8010Grid slot2009-05-05T14:00:21Z<p>Martoss: /* Syntax */</p>
<hr />
<div>== Overview ==<br />
Sets the grid slot location for a given object.<br />
<br />
== Syntax ==<br />
<source lang="python"><br />
set grid_slot, int, obj<br />
</source><br />
where '''int''' is the number of the grid slot and '''obj''' is the object to put there.<br />
<br />
Additionally, multiple objects can be assigned to the same grid slot by simply specifying different objects to the same grid slot. For example, if you have four objects loaded into PyMOL (A, B, C, D) and you want to show objects A and B in one slot while C and D are in another. Object E is shown in all slots by setting slot to -2:<br />
<br />
<source lang="python"><br />
set grid_slot, 1, A<br />
set grid_slot, 1, B<br />
set grid_slot, 2, C<br />
set grid_slot, 2, D<br />
set grid_slot, -2, E<br />
</source><br />
<br />
One use for this representation is in the context of structure prediction/validation (CASP) where you may want to show how your structure looks with respect to the native strucutre versus how somebody else's structure looks with respect to the native. Using grid_slot (as shown) will allow for a clearer, side-by-side comparison rather than the traditional superimposition of all three structures.<br />
<br />
== See Also ==<br />
[[grid_mode]]<br />
<br />
[[Category:Settings|Grid_slot]]</div>Martosshttps://wiki.pymol.org/index.php?title=Ideas&diff=11792Ideas2008-05-23T12:19:44Z<p>Martoss: /* Low-Level Enhancement Ideas (Mostly C-oriented) */</p>
<hr />
<div>=== Ideas for PyMOL Development ===<br />
<br />
This page was originally developed for the 2008 Google Summer of Code competition, but seeing as PyMOL wasn't selected, this page can instead serve as a resource for ongoing PyMOL development efforts.<br />
<br />
== Where to Start ==<br />
<br />
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. <br />
<br />
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.<br />
<br />
== Choosing a Topic ==<br />
<br />
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!<br />
<br />
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.<br />
<br />
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.<br />
<br />
== Integration Ideas (Linking Out to Useful Open-Source Tools) ==<br />
<br />
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.<br />
<br />
* APBS (electrostatics calculations): Improve the existing plugin. Michael Lerner is currently leading this effort. See [[APBS]]<br />
* 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]<br />
* mengine (MMFF small molecule cleanup): work is in progress (Delsci).<br />
* mpeg_encode (MPEG movie production on Linux, etc.): work is in progress (Delsci).<br />
* GIMP (image manipulation): Streamline & document the process of exporting images from PyMOL into GIMP and preparing them for submission to scientific Journals.<br />
* Blender (general-purpose 3D modeling & animation): Streamline & document the process of getting molecular geometry out of PyMOL and into Blender.<br />
* Jmol (publishing visualizations inside of web pages): Liason between PyMOL & Jmol projects to develop a shared molecular visualization data model compatible with both applications.<br />
* Firefox (plugin): Develop an PyMOL plugin compatible with Firefox.<br />
* MMTK (molecular mechanics -- Python/flexible): Develop the ability to round-trip molecular systems from PyMOL, into MMTK, and back.<br />
* 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]<br />
* OpenOffice (escape Microsoft hegemony): Develop an PyMOL plugin.<br />
* IPython integration (interactive shell): a robust alternative to the PyMOL command line?<br />
* R (statistics): PyMOL a 3D viewer environment for visualizating & manipulating large statistical data sets?<br />
<br />
Are there other key open-source packages we might specifically target for integration with PyMOL, either through GSoC or beyond?<br />
<br />
== High-Level Enhancement Ideas (Mostly Python-oriented) ==<br />
<br />
* Work on [[#More Ideas (Please add your own!)| [MolViz]]]<br />
* Develop new plugins which automate routine tasks.<br />
* Improve the Python API documentation.<br />
* Flesh out the new "from pymol2 import PyMOL" instance-based PyMOL API.<br />
* Develop alternate Tkinter "skins" (for custom OEM-like applications).<br />
* Develop a Tkinter/TOGL widget which holds a PyMOL viewer instance.<br />
* Develop a PyQt widget which holds a PyMOL viewer instance.<br />
* 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.<br />
* Add a plugin for a GUI window with the same functionality as the "Control Panel" window in SwissPDB Viewer.<br />
* Extend and modify the PyMOL command language so as to be compatible with existing RasMol and/or Jmol scripts.<br />
* Enhance the Mutagenesis Wizard in order to support Nucleic acids and/or Sugars.<br />
* Streamline the process of creating movies out of Scenes.<br />
<br />
== Low-Level Enhancement Ideas (Mostly C-oriented) ==<br />
<br />
* Provide a "split" view with multiple molecules each in their own pane (already partially implemented).<br />
* Add a movie slider similar to that found in Maya, Cinema4D, 3DSMax.<br />
* Enable editing of displayed sequence alignments.<br />
* Add multi-line textual annotations<br />
* Support additional annotation object including: arrow, lines, and blobs.<br />
* Add display of secondary structure into the sequence viewer.<br />
* Enable per-object Z clipping (especially in the ray tracer)<br />
* Hilite H-bonds, salt bridges, Pi-stacking, Pi-cations, etc.<br />
* Build in a simple forcefield and energy minimizer suitable for use with Mutagenesis.<br />
* Improve the ability to animate objects independently when creating movies.<br />
* Incorporate a suite of standard NMR visualizations (restraint violations, per-residue RMS, etc.)<br />
* Enumeration and display of low-energy conformers.<br />
* Automated structure grafting (poor-man's homology modeling).<br />
* Import of alignment files.<br />
* Implement IMD (Interactive Molecular Dynamics) Interface, see http://www.ks.uiuc.edu/Research/vmd/imd/<br />
<br />
== Difficult C-level Code Refactoring Ideas ==<br />
<br />
* Assemble a test suite which thoroughly exercises the existing code (a prerequisite to major refactoring).<br />
* Catch & handle memory-allocation failures gracefully (instead of crashing).<br />
* Replace PyMOL's memory management & custom containers with a simple runtime object model.<br />
* Separate the View and the Controllers from the Model so that they can all run asynchronously (on multiple cores).<br />
* Enable generalized undo of changes made to the Model.<br />
* Clean up the internal matrix handling code.<br />
<br />
== Ideas Involving Proprietary APIs ==<br />
<br />
Since these involve closed-source APIs and infrastructure, they aren't suitable for open-source development efforts. However, such requests are noted here for the sake of complete coverage.<br />
<br />
* Build an ActiveX Control for PowerPoint and/or Internet Explorer (work is in progress - Delsci)<br />
* Support direct export of Windows Media files (AVI movies).<br />
* 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.<br />
* Integrate directly via Mathematica via MathLink.<br />
* Further enhance JyMOL (Java-JNI/wrapped PyMOL)<br />
* Integrate with Matlab.<br />
<br />
== More Ideas (Please add your own!) ==<br />
* [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 [[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:<br />
** Improving the existing [[ImmersiveViz]] PyMol plugin for more precise control of the environment.<br />
** Developing new input drivers for the Wiimote form of control. This would require some bluetooth hacking.<br />
** 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).<br />
* Provide a 2D chemical depiction of the current 3D view.<br />
* Spreadsheet view with additional information (e.g. IC50's).<br />
* Create additional documentation, screen casts, & tutorials.<br />
* Export 3D PDF images.<br />
* Add extra "Single Word Selectors" like "nucleic", "protein", "water", "ions", "backbone" (for nucleic acids or proteins), "mainchain", "sidechain"</div>Martosshttps://wiki.pymol.org/index.php?title=Pdb_retain_ids&diff=7163Pdb retain ids2008-04-24T23:00:10Z<p>Martoss: New page: == Overview == If set, atoms and residues are not renumbered when exported imported pdb. (Must be set before import) == Syntax == <source lang="python"> set pdb_retain_ids,[0,1] set pdb...</p>
<hr />
<div>== Overview ==<br />
<br />
If set, atoms and residues are not renumbered when exported imported pdb. (Must be set before import)<br />
<br />
== Syntax ==<br />
<br />
<source lang="python"><br />
set pdb_retain_ids,[0,1]<br />
set pdb_retain_ids #default 1<br />
</source><br />
<br />
== Example ==<br />
<br />
Loaded and exported with pdb_retain_ids set to 0<br />
<source lang="diff"><br />
ATOM 21 CH2 TRP A 2 38.350 22.030 11.200 1.00 0.00 C<br />
ATOM 22 HH2 TRP A 2 38.620 21.010 10.930 1.00 0.00 H<br />
ATOM 23 C TRP A 2 35.010 27.370 14.910 1.00 0.00 C<br />
ATOM 24 O TRP A 2 35.380 27.560 16.060 1.00 0.00 O<br />
ATOM 25 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C<br />
ATOM 26 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H<br />
ATOM 27 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H<br />
ATOM 28 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H<br />
ATOM 29 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C<br />
ATOM 30 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O<br />
TER 31 ACE A 1 <br />
ATOM 32 N TRP A 3 33.910 27.930 14.400 1.00 0.00 N<br />
ATOM 33 H TRP A 3 33.670 27.680 13.450 1.00 0.00 H<br />
ATOM 34 CA TRP A 3 33.080 28.950 15.030 1.00 0.00 C<br />
<br />
</source><br />
Loaded and exported with pdb_retain_ids set to 1<br />
<source lang="diff"><br />
ATOM 27 CH2 TRP A 2 38.350 22.030 11.200 1.00 0.00 C<br />
ATOM 28 HH2 TRP A 2 38.620 21.010 10.930 1.00 0.00 H<br />
ATOM 29 C TRP A 2 35.010 27.370 14.910 1.00 0.00 C<br />
ATOM 30 O TRP A 2 35.380 27.560 16.060 1.00 0.00 O<br />
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C<br />
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H<br />
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H<br />
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H<br />
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C<br />
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O<br />
TER 7 ACE A 1 <br />
ATOM 31 N TRP A 3 33.910 27.930 14.400 1.00 0.00 N<br />
ATOM 32 H TRP A 3 33.670 27.680 13.450 1.00 0.00 H<br />
ATOM 33 CA TRP A 3 33.080 28.950 15.030 1.00 0.00 C<br />
</source><br />
<br />
[[Category:Settings|Retain Order]]</div>Martosshttps://wiki.pymol.org/index.php?title=Retain_order&diff=9470Retain order2008-04-24T22:48:15Z<p>Martoss: /* Overview */</p>
<hr />
<div>== Overview ==<br />
<br />
If set, order is preserved when expoting an imported pdb. (Must be set before import)<br />
<br />
== Syntax ==<br />
<br />
<source lang="python"><br />
set retain_order,[0,1]<br />
set retain_order #default 1<br />
</source><br />
<br />
== Example ==<br />
<br />
Original PDB:<br />
<br />
<source lang="diff"><br />
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00<br />
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00<br />
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00<br />
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00<br />
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00<br />
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00<br />
</source><br />
<br />
Loaded and exported with retain_order set to 0<br />
<source lang="diff"><br />
ATOM 1 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C<br />
ATOM 2 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O<br />
ATOM 3 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C<br />
ATOM 4 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H<br />
ATOM 5 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H<br />
ATOM 6 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H<br />
</source><br />
Loaded and exported with retain_order set to 1<br />
<source lang="diff"><br />
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C<br />
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H<br />
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H<br />
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H<br />
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C<br />
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O<br />
</source><br />
<br />
[[Category:Settings|Retain Order]]</div>Martosshttps://wiki.pymol.org/index.php?title=Retain_order&diff=9469Retain order2008-04-24T22:47:17Z<p>Martoss: </p>
<hr />
<div>== Overview ==<br />
<br />
set reflect controls the amount of light reflection and the effect directional light therefore has on shadows and the general lighting of the scene.<br />
<br />
== Syntax ==<br />
<br />
<source lang="python"><br />
set retain_order,[0,1]<br />
set retain_order #default 1<br />
</source><br />
<br />
== Example ==<br />
<br />
Original PDB:<br />
<br />
<source lang="diff"><br />
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00<br />
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00<br />
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00<br />
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00<br />
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00<br />
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00<br />
</source><br />
<br />
Loaded and exported with retain_order set to 0<br />
<source lang="diff"><br />
ATOM 1 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C<br />
ATOM 2 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O<br />
ATOM 3 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C<br />
ATOM 4 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H<br />
ATOM 5 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H<br />
ATOM 6 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H<br />
</source><br />
Loaded and exported with retain_order set to 1<br />
<source lang="diff"><br />
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C<br />
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H<br />
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H<br />
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H<br />
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C<br />
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O<br />
</source><br />
<br />
[[Category:Settings|Retain Order]]</div>Martosshttps://wiki.pymol.org/index.php?title=Retain_order&diff=9468Retain order2008-04-24T22:46:28Z<p>Martoss: </p>
<hr />
<div>== Overview ==<br />
<br />
set reflect controls the amount of light reflection and the effect directional light therefore has on shadows and the general lighting of the scene.<br />
<br />
== Syntax ==<br />
<br />
<source lang="python"><br />
set retain_order,[0,1]<br />
set retain_order #default 1<br />
</source><br />
<br />
== Example ==<br />
<br />
Original PDB:<br />
<br />
<source><br />
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00<br />
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00<br />
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00<br />
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00<br />
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00<br />
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00<br />
</source><br />
<br />
Loaded and exported with retain_order set to 0<br />
<source><br />
ATOM 1 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C<br />
ATOM 2 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O<br />
ATOM 3 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C<br />
ATOM 4 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H<br />
ATOM 5 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H<br />
ATOM 6 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H<br />
</source><br />
Loaded and exported with retain_order set to 1<br />
<source><br />
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C<br />
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H<br />
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H<br />
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H<br />
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C<br />
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O<br />
</source><br />
<br />
[[Category:Settings|Retain Order]]</div>Martosshttps://wiki.pymol.org/index.php?title=Retain_order&diff=9467Retain order2008-04-24T22:45:37Z<p>Martoss: New page: == Overview == set reflect controls the amount of light reflection and the effect directional light therefore has on shadows and the general lighting of the scene. == Syntax == <source ...</p>
<hr />
<div>== Overview ==<br />
<br />
set reflect controls the amount of light reflection and the effect directional light therefore has on shadows and the general lighting of the scene.<br />
<br />
== Syntax ==<br />
<br />
<source lang="python"><br />
set retain_order,[0,1]<br />
set retain_order #default 1<br />
</source><br />
<br />
== Example ==<br />
<br />
Original PDB:<br />
<br />
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00<br />
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00<br />
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00<br />
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00<br />
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00<br />
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00<br />
<br />
Loaded and exported with retain_order set to 0<br />
<br />
ATOM 1 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C<br />
ATOM 2 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O<br />
ATOM 3 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C<br />
ATOM 4 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H<br />
ATOM 5 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H<br />
ATOM 6 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H<br />
<br />
Loaded and exported with retain_order set to 1<br />
<br />
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C<br />
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H<br />
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H<br />
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H<br />
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C<br />
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O<br />
<br />
<br />
[[Category:Settings|Retain Order]]</div>Martosshttps://wiki.pymol.org/index.php?title=Settings&diff=10145Settings2008-04-24T22:34:08Z<p>Martoss: </p>
<hr />
<div>PyMOL is incredible useful because of its flexibility. Almost any setting can be tweaked to give you the ability to make your scenes appear just as you want. Each command usually comes with one or more settings. For example, the [[ray]] command comes with '''50''' settings!<br />
<br />
Below you will find the list of all known settings (as of this writing). Settings are added all the time, so this list should be updated somehow. Also, see all '''[[:Category:Settings|documented settings]]'''.<br />
<br />
If you feel like documenting them, and what they do, feel free.<br />
<br />
active_selections ray_default_renderer <br />
[[all_states]] ray_direct_shade <br />
[[ambient]] ray_hint_camera <br />
angle_label_position ray_hint_shadow <br />
angle_size ray_improve_shadows <br />
animation ray_interior_color <br />
animation_duration ray_interior_mode <br />
[[antialias]] ray_interior_reflect <br />
async_builds ray_interior_shadows <br />
[[atom_name_wildcard]] ray_interior_texture <br />
auto_classify_atoms ray_legacy_lighting <br />
auto_color ray_max_passes <br />
auto_dss [[ray_opaque_background]] <br />
auto_hide_selections [[ray_orthoscopic]] <br />
auto_indicate_flags ray_oversample_cutoff <br />
auto_number_selections ray_pixel_scale <br />
auto_remove_hydrogens [[ray_shadow]] <br />
auto_sculpt ray_shadow_decay_factor <br />
auto_show_lines ray_shadow_decay_range <br />
auto_show_nonbonded ray_shadow_fudge <br />
auto_show_selections [[ray_shadows]] <br />
auto_show_spheres ray_texture <br />
[[auto_zoom]] ray_texture_settings <br />
[[backface_cull]] ray_trace_depth_factor <br />
batch_prefix ray_trace_disco_factor <br />
[[bg_rgb]] [[ray_trace_fog]] <br />
bonding_vdw_cutoff ray_trace_fog_start <br />
button_mode [[ray_trace_frames]] <br />
button_mode_name ray_trace_gain <br />
cache_display [[Ray#Modes|ray_trace_mode]]<br />
cache_frames ray_trace_slope_factor <br />
cache_memory ray_transparency_contrast <br />
[[cartoon_color]] ray_transparency_shadows <br />
[[Cartoon Helix Settings|cartoon_cylindrical_helices]] ray_transparency_spec_cut <br />
cartoon_debug ray_transparency_specular <br />
[[cartoon_discrete_colors]] ray_triangle_fudge <br />
[[cartoon_dumbbell_length]] [[reflect]] <br />
[[cartoon_dumbbell_radius]] reflect_power <br />
[[cartoon_dumbbell_width]] [[retain_order]] <br />
[[Cartoon Helix Settings|cartoon_fancy_helices]] [[ribbon_color]] <br />
[[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode <br />
[[cartoon_flat_cycles]] ribbon_power <br />
[[cartoon_flat_sheets]] ribbon_power_b <br />
[[Cartoon_helix_radius]] ribbon_radius <br />
[[cartoon_highlight_color]] [[ribbon_sampling]] <br />
cartoon_ladder_color ribbon_side_chain_helper <br />
cartoon_ladder_mode [[ribbon_smooth]] <br />
cartoon_ladder_radius ribbon_throw <br />
cartoon_loop_cap ribbon_trace_atoms <br />
cartoon_loop_quality [[ribbon_width]] <br />
cartoon_loop_radius robust_logs <br />
[[cartoon_nucleic_acid_color]] rock_delay <br />
[[cartoon_nucleic_acid_mode]] roving_byres <br />
[[cartoon_oval_length]] roving_cartoon <br />
[[cartoon_oval_quality]] roving_delay <br />
[[cartoon_oval_width]] roving_detail <br />
cartoon_power roving_isomesh <br />
cartoon_power_b roving_isosurface <br />
cartoon_putty_quality roving_labels <br />
cartoon_putty_radius roving_lines <br />
cartoon_putty_range roving_map1_level <br />
cartoon_putty_scale_max roving_map1_name <br />
cartoon_putty_scale_min roving_map2_level <br />
cartoon_putty_scale_power roving_map2_name <br />
[[cartoon_rect_length]] roving_map3_level <br />
[[cartoon_rect_width]] roving_map3_name <br />
cartoon_refine roving_nb_spheres <br />
cartoon_refine_normals roving_nonbonded <br />
cartoon_refine_tips roving_origin <br />
cartoon_ring_color roving_origin_z <br />
cartoon_ring_finder roving_origin_z_cushion <br />
[[cartoon_ring_mode]] roving_polar_contacts <br />
cartoon_ring_radius roving_polar_cutoff <br />
[[cartoon_ring_transparency]] roving_ribbon <br />
cartoon_ring_width roving_selection <br />
[[cartoon_round_helices]] roving_spheres <br />
[[cartoon_sampling]] roving_sticks <br />
[[cartoon_side_chain_helper]] scene_animation <br />
cartoon_smooth_cycles scene_animation_duration <br />
cartoon_smooth_first scene_current_name <br />
cartoon_smooth_last scene_loop <br />
[[cartoon_smooth_loops]] scene_restart_movie_delay <br />
cartoon_throw scenes_changed <br />
cartoon_trace_atoms sculpt_angl_weight <br />
[[cartoon_transparency]] sculpt_auto_center <br />
cartoon_tube_cap sculpt_avd_excl <br />
cartoon_tube_quality sculpt_avd_gap <br />
cartoon_tube_radius sculpt_avd_range <br />
[[cavity_cull]] sculpt_avd_weight <br />
cgo_dot_radius sculpt_bond_weight <br />
cgo_dot_width sculpt_field_mask <br />
cgo_line_radius sculpt_hb_overlap <br />
cgo_line_width sculpt_hb_overlap_base <br />
cgo_ray_width_scale sculpt_line_weight <br />
cgo_sphere_quality sculpt_max_max <br />
cgo_transparency sculpt_max_min <br />
clamp_colors sculpt_max_scale <br />
connect_bonded sculpt_max_weight <br />
connect_cutoff sculpt_memory <br />
connect_mode sculpt_min_max <br />
coulomb_cutoff sculpt_min_min <br />
coulomb_dielectric sculpt_min_scale <br />
coulomb_units_factor sculpt_min_weight <br />
cull_spheres sculpt_nb_interval <br />
[[Dash_Gap]] sculpt_plan_weight <br />
[[Dash_Length]] sculpt_pyra_weight <br />
[[Dash_Radius]] sculpt_tors_tolerance <br />
[[Dash_Round_Ends]] sculpt_tors_weight <br />
dash_width sculpt_tri_max <br />
debug_pick sculpt_tri_min <br />
defer_builds_mode sculpt_tri_mode <br />
defer_updates sculpt_tri_scale <br />
[[depth_cue]] sculpt_tri_weight <br />
dihedral_label_position sculpt_vdw_scale <br />
dihedral_size sculpt_vdw_scale14 <br />
direct sculpt_vdw_vis_max <br />
dist_counter sculpt_vdw_vis_mid <br />
distance_exclusion sculpt_vdw_vis_min <br />
dot_color sculpt_vdw_vis_mode <br />
dot_density sculpt_vdw_weight <br />
dot_hydrogens sculpt_vdw_weight14 <br />
dot_lighting sculpting <br />
dot_mode sculpting_cycles <br />
dot_normals secondary_structure <br />
[[dot_radius]] security <br />
dot_solvent sel_counter<br />
[[dot_width]] selection_overlay <br />
draw_frames selection_round_points <br />
editor_auto_dihedral selection_visible_only <br />
editor_auto_origin [[selection_width]] <br />
editor_label_fragments selection_width_max <br />
fast_idle selection_width_scale <br />
fetch_path [[seq_view]] <br />
[[Field_Of_View]] seq_view_alignment <br />
fit_iterations seq_view_color <br />
fit_tolerance seq_view_discrete_by_state <br />
float_labels seq_view_fill_char <br />
[[fog]] seq_view_fill_color <br />
[[fog_start]] seq_view_format <br />
frame seq_view_label_color <br />
full_screen seq_view_label_mode <br />
gamma seq_view_label_spacing <br />
gaussian_b_adjust seq_view_label_start <br />
gaussian_b_floor [[seq_view_location]] <br />
gaussian_resolution seq_view_overlay <br />
gl_ambient seq_view_unaligned_color <br />
[[grid_mode]]<br />
[[grid_slot]]<br />
h_bond_cone seq_view_unaligned_mode <br />
h_bond_cutoff_center session_file <br />
h_bond_cutoff_edge session_migration <br />
h_bond_exclusion session_version_check <br />
h_bond_max_angle [[shininess]]<br />
h_bond_power_a show_alpha_checker <br />
h_bond_power_b show_progress <br />
[[half_bonds]] simplify_display_lists <br />
[[hash_max]] single_image <br />
hide_underscore_names slice_dynamic_grid <br />
idle_delay slice_dynamic_grid_resolution<br />
ignore_case slice_grid <br />
ignore_pdb_segi slice_height_map <br />
image_dots_per_inch slice_height_scale <br />
internal_feedback slice_track_camera <br />
[[Internal Gui|internal_gui]] slow_idle <br />
internal_gui_control_size smooth_color_triangle <br />
internal_gui_mode solvent_radius <br />
internal_gui_width spec_count <br />
[[internal_prompt]] spec_direct <br />
isomesh_auto_state spec_direct_power <br />
[[label_color]] spec_power <br />
[[Label_font_id]] [[spec_reflect]] <br />
[[Label_outline_color]] specular <br />
[[label_position]] specular_intensity <br />
[[label_shadow_mode]] [[sphere_color]] <br />
[[label_size]] [[sphere_mode]] <br />
legacy_mouse_zoom sphere_point_max_size <br />
legacy_vdw_radii sphere_point_size <br />
light [[sphere_quality]] <br />
light2 [[sphere_scale]] <br />
light3 sphere_solvent <br />
light4 [[sphere_transparency]] <br />
light5 spheroid_fill <br />
light6 spheroid_scale <br />
light7 spheroid_smooth <br />
light8 ss_helix_phi_exclude <br />
light9 ss_helix_phi_include <br />
[[light_count]] ss_helix_phi_target <br />
line_radius ss_helix_psi_exclude <br />
[[line_smooth]] ss_helix_psi_include <br />
line_stick_helper ss_helix_psi_target <br />
line_width ss_strand_phi_exclude <br />
log_box_selections ss_strand_phi_include <br />
log_conformations ss_strand_phi_target <br />
logging ss_strand_psi_exclude <br />
matrix_mode ss_strand_psi_include <br />
max_threads ss_strand_psi_target <br />
max_triangles state <br />
[[mesh_color]] static_singletons <br />
[[mesh_lighting]] [[stereo]]<br />
[[mesh_mode]] [[stereo_angle]]<br />
mesh_normals stereo_double_pump_mono <br />
[[mesh_quality]] [[stereo_mode]] <br />
mesh_radius stereo_shift <br />
mesh_solvent [[stick_ball]] <br />
[[mesh_type]] [[stick_ball_ratio]] <br />
[[mesh_width]] [[stick_color]]<br />
[[min_mesh_spacing]] stick_fixed_radius <br />
mouse_limit [[stick_nub]] <br />
mouse_restart_movie_delay stick_overlap <br />
mouse_scale stick_quality <br />
mouse_selection_mode stick_radius <br />
movie_delay [[stick_transparency]] <br />
movie_loop stick_valence_scale <br />
multiplex stop_on_exceptions <br />
no_idle surface_best <br />
nonbonded_size surface_carve_cutoff <br />
normal_workaround surface_carve_selection <br />
normalize_ccp4_maps surface_carve_state <br />
normalize_grd_maps surface_circumscribe <br />
normalize_o_maps surface_clear_cutoff <br />
nvidia_bugs surface_clear_selection <br />
opaque_background surface_clear_state <br />
[[orthoscopic]] surface_color <br />
overlay surface_debug <br />
overlay_lines surface_miserable <br />
pdb_conect_all [[surface_mode]] <br />
pdb_discrete_chains surface_normal <br />
pdb_echo_tags surface_optimize_subsets <br />
pdb_hetatm_sort surface_poor <br />
pdb_honor_model_number surface_proximity <br />
pdb_insertions_go_first surface_quality <br />
pdb_insure_orthogonal surface_ramp_above_mode <br />
pdb_literal_names surface_solvent <br />
pdb_no_end_record surface_trim_cutoff <br />
pdb_reformat_names_mode surface_trim_factor <br />
[[pdb_retain_ids]] surface_type <br />
pdb_standard_order suspend_updates <br />
pdb_truncate_residue_name swap_dsn6_bytes <br />
pdb_unbond_cations sweep_angle <br />
pdb_use_ter_records sweep_mode <br />
[[pickable]] sweep_phase <br />
png_file_gamma sweep_speed <br />
png_screen_gamma test1 <br />
power test2 <br />
pqr_no_chain_id text <br />
presentation texture_fonts <br />
presentation_auto_quit [[transparency]] <br />
presentation_auto_start transparency_mode <br />
presentation_mode transparency_picking_mode <br />
preserve_chempy_ids triangle_max_passes <br />
pymol_space_max_blue trim_dots <br />
pymol_space_max_green [[two_sided_lighting]]<br />
pymol_space_max_red use_display_lists <br />
pymol_space_min_factor [[valence]] <br />
raise_exceptions valence_default <br />
rank_assisted_sorts valence_size <br />
ray_blend_blue validate_object_names <br />
ray_blend_colors [[virtual_trackball]] <br />
ray_blend_green wildcard <br />
ray_blend_red wizard_prompt_mode <br />
ray_color_ramps wrap_output <br />
<br />
[[Category:Settings|All Settings]]</div>Martosshttps://wiki.pymol.org/index.php?title=APBS&diff=3710APBS2007-01-20T23:48:33Z<p>Martoss: /* Installing the Dependencies on Linux */</p>
<hr />
<div>== Introduction ==<br />
[[Image:Rna_surface_apbs.png|thumb|APBS-generated electrostatic surface displayed in PyMOL]]<br />
[http://apbs.sourceforge.net APBS], the Adaptive Poisson-Boltzmann Solver, is a [http://www.oreilly.com/openbook/freedom/ freely] available macromolecular electrostatics calculation program released under the [http://www.gnu.org/copyleft/gpl.html GPL]. It is a cost-effective but uncompromised alternative to [http://trantor.bioc.columbia.edu/grasp/ GRASP], and it can be used within pymol. Pymol can display the results of the calculations as an electrostatic potential molecular surface.<br />
<br />
PyMol currently supports the '''APBS plugin''' written by Michael Lerner. This plugin makes it possible to run APBS from within PyMOL, and then display the results as a color-coded electrostatic surface (units k<sub>b</sub>T/e<sub>c</sub>) in the molecular display window (as with the image to the right). See [http://www-personal.umich.edu/~mlerner/PyMOL/ Michael Lerner's Page] for more details, including instructions on how to download, install and use the plugin.<br />
<br />
'''Nucleic acids may prove problematic for the apbs plugin.''' If so, use the [http://pdb2pqr.sourceforge.net/ pdb2pqr] command-line tool to create a pqr file manually, instead of using the plugin to generate it. Then direct the APBS GUI on the [http://www-personal.umich.edu/~mlerner/PyMOL/images/main.png main menu] to read the pqr file you '''externally generated.'''<br />
<br />
==Required Dependencies==<br />
[http://apbs.sourceforge.net APBS] and its dependencies like [http://pdb2pqr.sourceforge.net pdb2pqr] and [http://scicomp.ucsd.edu/~mholst/codes/maloc/ maloc] are [http://www.oreilly.com/openbook/freedom/ freely] available under the [http://www.gnu.org/copyleft/gpl.html GPL]. The author of the software however [http://agave.wustl.edu/apbs/download/ asks that users register] with him to aid him in obtaining grant funding.<br />
<br />
----<br />
===Installing the Dependencies on OS X===<br />
#First, [http://agave.wustl.edu/apbs/download/ register] your use of the software. This will keep everyone happy.<br />
#Second, if you don't already have the [http://fink.sourceforge.net fink package management system], now is a good time to get it. Here is a [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Quick_Start quick-start set of instructions] for getting X-windows, compilers, and fink all installed. <br />
#Once you are up and going, [http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/How_to_Activate_the_Unstable_Branch activate the unstable branch in fink], and then issue the commands<br />
<br />
fink self-update<br />
fink install apbs<br />
<br />
or if you want to use the multi-processor version, issue<br />
<br />
fink self-update<br />
fink install apbs<br />
<br />
Then install the X-windows based version of pymol using the command<br />
<br />
fink install pymol-py24<br />
<br />
Note that the fink version of pymol '''already has''' the latest version of the APBS plugin. You are set to go!<br />
<br />
Further details, as well as screen shots, are given [http://www.pymolwiki.org/index.php/MAC_Install#Install_APBS_and_friends_with_fink elsewhere in this wiki].<br />
<br />
----<br />
<br />
===Installing the Dependencies on Linux===<br />
<br />
====RPMs====<br />
<br />
A variety of RPMs are available from the [http://sourceforge.net/project/showfiles.php?group_id=148472&package_id=163734&release_id=378273 APBS downloads website]. Again, please [http://agave.wustl.edu/apbs/download/ register] your use of the software if you have not yet done so.<br />
<br />
====Debian packages====<br />
<br />
For ubuntu and other debian linux distributions, probably the simplest thing is to download a promising looking rpm, convert it with the program [http://kitenet.net/programs/alien/ alien], and then install the [http://xanana.ucsc.edu/linux newly generated debian package] with the command<br />
<br />
sudo dpkg -i apbs*.deb<br />
<br />
====Gentoo====<br />
<br />
You have to install apbs and pdb2pqr. Both are masked via keywords atm. Type as root:<br />
<br />
echo sci-chemistry/pdb2pqr >> /etc/portage/packages.keywords<br />
<br />
echo sci-chemistry/apbs >> /etc/portage/packages.keywords<br />
<br />
emerge -av sci-chemistry/apbs sci-chemistry/pdb2pqr<br />
<br />
----<br />
<br />
==Further contributions and edits are needed.==</div>Martoss