PyMOL Wiki - User contributions [en]

Grid slot

2009-05-05T14:00:21Z

Martoss: /* Syntax */

== Overview ==
Sets the grid slot location for a given object.

== Syntax ==
<source lang="python">
set grid_slot, int, obj
</source>
where '''int''' is the number of the grid slot and '''obj''' is the object to put there.

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:

<source lang="python">
set grid_slot, 1, A
set grid_slot, 1, B
set grid_slot, 2, C
set grid_slot, 2, D
set grid_slot, -2, E
</source>

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.

== See Also ==
[[grid_mode]]

[[Category:Settings|Grid_slot]]

Ideas

2008-05-23T12:19:44Z

Martoss: /* Low-Level Enhancement Ideas (Mostly C-oriented) */

=== Ideas for PyMOL Development ===

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.

== 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.
* Implement IMD (Interactive Molecular Dynamics) Interface, see http://www.ks.uiuc.edu/Research/vmd/imd/

== 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 open-source development efforts. However, such requests are noted here for the sake of complete coverage.

* 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 [[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 [[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.
* Add extra "Single Word Selectors" like "nucleic", "protein", "water", "ions", "backbone" (for nucleic acids or proteins), "mainchain", "sidechain"

Pdb retain ids

2008-04-24T23:00:10Z

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...

== 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_retain_ids #default 1
</source>

== Example ==

Loaded and exported with pdb_retain_ids set to 0
<source lang="diff">
ATOM 21 CH2 TRP A 2 38.350 22.030 11.200 1.00 0.00 C
ATOM 22 HH2 TRP A 2 38.620 21.010 10.930 1.00 0.00 H
ATOM 23 C TRP A 2 35.010 27.370 14.910 1.00 0.00 C
ATOM 24 O TRP A 2 35.380 27.560 16.060 1.00 0.00 O
ATOM 25 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C
ATOM 26 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H
ATOM 27 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H
ATOM 28 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H
ATOM 29 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C
ATOM 30 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O
TER 31 ACE A 1
ATOM 32 N TRP A 3 33.910 27.930 14.400 1.00 0.00 N
ATOM 33 H TRP A 3 33.670 27.680 13.450 1.00 0.00 H
ATOM 34 CA TRP A 3 33.080 28.950 15.030 1.00 0.00 C

</source>
Loaded and exported with pdb_retain_ids set to 1
<source lang="diff">
ATOM 27 CH2 TRP A 2 38.350 22.030 11.200 1.00 0.00 C
ATOM 28 HH2 TRP A 2 38.620 21.010 10.930 1.00 0.00 H
ATOM 29 C TRP A 2 35.010 27.370 14.910 1.00 0.00 C
ATOM 30 O TRP A 2 35.380 27.560 16.060 1.00 0.00 O
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O
TER 7 ACE A 1
ATOM 31 N TRP A 3 33.910 27.930 14.400 1.00 0.00 N
ATOM 32 H TRP A 3 33.670 27.680 13.450 1.00 0.00 H
ATOM 33 CA TRP A 3 33.080 28.950 15.030 1.00 0.00 C
</source>

[[Category:Settings|Retain Order]]

Retain order

2008-04-24T22:48:15Z

Martoss: /* Overview */

== Overview ==

If set, order is preserved when expoting an imported pdb. (Must be set before import)

== Syntax ==

<source lang="python">
set retain_order,[0,1]
set retain_order #default 1
</source>

== Example ==

Original PDB:

<source lang="diff">
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00
</source>

Loaded and exported with retain_order set to 0
<source lang="diff">
ATOM 1 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C
ATOM 2 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O
ATOM 3 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C
ATOM 4 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H
ATOM 5 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H
ATOM 6 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H
</source>
Loaded and exported with retain_order set to 1
<source lang="diff">
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O
</source>

[[Category:Settings|Retain Order]]

Retain order

2008-04-24T22:47:17Z

Martoss:

== 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 lang="python">
set retain_order,[0,1]
set retain_order #default 1
</source>

== Example ==

Original PDB:

<source lang="diff">
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00
</source>

Loaded and exported with retain_order set to 0
<source lang="diff">
ATOM 1 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C
ATOM 2 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O
ATOM 3 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C
ATOM 4 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H
ATOM 5 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H
ATOM 6 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H
</source>
Loaded and exported with retain_order set to 1
<source lang="diff">
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O
</source>

[[Category:Settings|Retain Order]]

Retain order

2008-04-24T22:46:28Z

Martoss:

== 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 lang="python">
set retain_order,[0,1]
set retain_order #default 1
</source>

== Example ==

Original PDB:

<source>
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00
</source>

Loaded and exported with retain_order set to 0
<source>
ATOM 1 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C
ATOM 2 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O
ATOM 3 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C
ATOM 4 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H
ATOM 5 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H
ATOM 6 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H
</source>
Loaded and exported with retain_order set to 1
<source>
ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O
</source>

[[Category:Settings|Retain Order]]

Retain order

2008-04-24T22:45:37Z

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 ...

== 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 lang="python">
set retain_order,[0,1]
set retain_order #default 1
</source>

== Example ==

Original PDB:

ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00

Loaded and exported with retain_order set to 0

ATOM 1 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C
ATOM 2 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O
ATOM 3 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C
ATOM 4 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H
ATOM 5 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H
ATOM 6 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H

Loaded and exported with retain_order set to 1

ATOM 1 CH3 ACE A 1 33.160 24.100 12.400 1.00 0.00 C
ATOM 2 HH31 ACE A 1 32.860 24.830 11.650 1.00 0.00 H
ATOM 3 HH32 ACE A 1 33.800 23.390 11.880 1.00 0.00 H
ATOM 4 HH33 ACE A 1 32.250 23.650 12.770 1.00 0.00 H
ATOM 5 C ACE A 1 33.910 24.800 13.510 1.00 0.00 C
ATOM 6 O ACE A 1 33.760 24.560 14.700 1.00 0.00 O

[[Category:Settings|Retain Order]]

Settings

2008-04-24T22:34:08Z

Martoss:

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!

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]]'''.

If you feel like documenting them, and what they do, feel free.

active_selections ray_default_renderer
[[all_states]] ray_direct_shade
[[ambient]] ray_hint_camera
angle_label_position ray_hint_shadow
angle_size ray_improve_shadows
animation ray_interior_color
animation_duration ray_interior_mode
[[antialias]] ray_interior_reflect
async_builds ray_interior_shadows
[[atom_name_wildcard]] ray_interior_texture
auto_classify_atoms ray_legacy_lighting
auto_color ray_max_passes
auto_dss [[ray_opaque_background]]
auto_hide_selections [[ray_orthoscopic]]
auto_indicate_flags ray_oversample_cutoff
auto_number_selections ray_pixel_scale
auto_remove_hydrogens [[ray_shadow]]
auto_sculpt ray_shadow_decay_factor
auto_show_lines ray_shadow_decay_range
auto_show_nonbonded ray_shadow_fudge
auto_show_selections [[ray_shadows]]
auto_show_spheres ray_texture
[[auto_zoom]] ray_texture_settings
[[backface_cull]] ray_trace_depth_factor
batch_prefix ray_trace_disco_factor
[[bg_rgb]] [[ray_trace_fog]]
bonding_vdw_cutoff ray_trace_fog_start
button_mode [[ray_trace_frames]]
button_mode_name ray_trace_gain
cache_display [[Ray#Modes|ray_trace_mode]]
cache_frames ray_trace_slope_factor
cache_memory ray_transparency_contrast
[[cartoon_color]] ray_transparency_shadows
[[Cartoon Helix Settings|cartoon_cylindrical_helices]] ray_transparency_spec_cut
cartoon_debug ray_transparency_specular
[[cartoon_discrete_colors]] ray_triangle_fudge
[[cartoon_dumbbell_length]] [[reflect]]
[[cartoon_dumbbell_radius]] reflect_power
[[cartoon_dumbbell_width]] [[retain_order]]
[[Cartoon Helix Settings|cartoon_fancy_helices]] [[ribbon_color]]
[[cartoon_fancy_sheets]] ribbon_nucleic_acid_mode
[[cartoon_flat_cycles]] ribbon_power
[[cartoon_flat_sheets]] ribbon_power_b
[[Cartoon_helix_radius]] ribbon_radius
[[cartoon_highlight_color]] [[ribbon_sampling]]
cartoon_ladder_color ribbon_side_chain_helper
cartoon_ladder_mode [[ribbon_smooth]]
cartoon_ladder_radius ribbon_throw
cartoon_loop_cap ribbon_trace_atoms
cartoon_loop_quality [[ribbon_width]]
cartoon_loop_radius robust_logs
[[cartoon_nucleic_acid_color]] rock_delay
[[cartoon_nucleic_acid_mode]] roving_byres
[[cartoon_oval_length]] roving_cartoon
[[cartoon_oval_quality]] roving_delay
[[cartoon_oval_width]] roving_detail
cartoon_power roving_isomesh
cartoon_power_b roving_isosurface
cartoon_putty_quality roving_labels
cartoon_putty_radius roving_lines
cartoon_putty_range roving_map1_level
cartoon_putty_scale_max roving_map1_name
cartoon_putty_scale_min roving_map2_level
cartoon_putty_scale_power roving_map2_name
[[cartoon_rect_length]] roving_map3_level
[[cartoon_rect_width]] roving_map3_name
cartoon_refine roving_nb_spheres
cartoon_refine_normals roving_nonbonded
cartoon_refine_tips roving_origin
cartoon_ring_color roving_origin_z
cartoon_ring_finder roving_origin_z_cushion
[[cartoon_ring_mode]] roving_polar_contacts
cartoon_ring_radius roving_polar_cutoff
[[cartoon_ring_transparency]] roving_ribbon
cartoon_ring_width roving_selection
[[cartoon_round_helices]] roving_spheres
[[cartoon_sampling]] roving_sticks
[[cartoon_side_chain_helper]] scene_animation
cartoon_smooth_cycles scene_animation_duration
cartoon_smooth_first scene_current_name
cartoon_smooth_last scene_loop
[[cartoon_smooth_loops]] scene_restart_movie_delay
cartoon_throw scenes_changed
cartoon_trace_atoms sculpt_angl_weight
[[cartoon_transparency]] sculpt_auto_center
cartoon_tube_cap sculpt_avd_excl
cartoon_tube_quality sculpt_avd_gap
cartoon_tube_radius sculpt_avd_range
[[cavity_cull]] sculpt_avd_weight
cgo_dot_radius sculpt_bond_weight
cgo_dot_width sculpt_field_mask
cgo_line_radius sculpt_hb_overlap
cgo_line_width sculpt_hb_overlap_base
cgo_ray_width_scale sculpt_line_weight
cgo_sphere_quality sculpt_max_max
cgo_transparency sculpt_max_min
clamp_colors sculpt_max_scale
connect_bonded sculpt_max_weight
connect_cutoff sculpt_memory
connect_mode sculpt_min_max
coulomb_cutoff sculpt_min_min
coulomb_dielectric sculpt_min_scale
coulomb_units_factor sculpt_min_weight
cull_spheres sculpt_nb_interval
[[Dash_Gap]] sculpt_plan_weight
[[Dash_Length]] sculpt_pyra_weight
[[Dash_Radius]] sculpt_tors_tolerance
[[Dash_Round_Ends]] sculpt_tors_weight
dash_width sculpt_tri_max
debug_pick sculpt_tri_min
defer_builds_mode sculpt_tri_mode
defer_updates sculpt_tri_scale
[[depth_cue]] sculpt_tri_weight
dihedral_label_position sculpt_vdw_scale
dihedral_size sculpt_vdw_scale14
direct sculpt_vdw_vis_max
dist_counter sculpt_vdw_vis_mid
distance_exclusion sculpt_vdw_vis_min
dot_color sculpt_vdw_vis_mode
dot_density sculpt_vdw_weight
dot_hydrogens sculpt_vdw_weight14
dot_lighting sculpting
dot_mode sculpting_cycles
dot_normals secondary_structure
[[dot_radius]] security
dot_solvent sel_counter
[[dot_width]] selection_overlay
draw_frames selection_round_points
editor_auto_dihedral selection_visible_only
editor_auto_origin [[selection_width]]
editor_label_fragments selection_width_max
fast_idle selection_width_scale
fetch_path [[seq_view]]
[[Field_Of_View]] seq_view_alignment
fit_iterations seq_view_color
fit_tolerance seq_view_discrete_by_state
float_labels seq_view_fill_char
[[fog]] seq_view_fill_color
[[fog_start]] seq_view_format
frame seq_view_label_color
full_screen seq_view_label_mode
gamma seq_view_label_spacing
gaussian_b_adjust seq_view_label_start
gaussian_b_floor [[seq_view_location]]
gaussian_resolution seq_view_overlay
gl_ambient seq_view_unaligned_color
[[grid_mode]]
[[grid_slot]]
h_bond_cone seq_view_unaligned_mode
h_bond_cutoff_center session_file
h_bond_cutoff_edge session_migration
h_bond_exclusion session_version_check
h_bond_max_angle [[shininess]]
h_bond_power_a show_alpha_checker
h_bond_power_b show_progress
[[half_bonds]] simplify_display_lists
[[hash_max]] single_image
hide_underscore_names slice_dynamic_grid
idle_delay slice_dynamic_grid_resolution
ignore_case slice_grid
ignore_pdb_segi slice_height_map
image_dots_per_inch slice_height_scale
internal_feedback slice_track_camera
[[Internal Gui|internal_gui]] slow_idle
internal_gui_control_size smooth_color_triangle
internal_gui_mode solvent_radius
internal_gui_width spec_count
[[internal_prompt]] spec_direct
isomesh_auto_state spec_direct_power
[[label_color]] spec_power
[[Label_font_id]] [[spec_reflect]]
[[Label_outline_color]] specular
[[label_position]] specular_intensity
[[label_shadow_mode]] [[sphere_color]]
[[label_size]] [[sphere_mode]]
legacy_mouse_zoom sphere_point_max_size
legacy_vdw_radii sphere_point_size
light [[sphere_quality]]
light2 [[sphere_scale]]
light3 sphere_solvent
light4 [[sphere_transparency]]
light5 spheroid_fill
light6 spheroid_scale
light7 spheroid_smooth
light8 ss_helix_phi_exclude
light9 ss_helix_phi_include
[[light_count]] ss_helix_phi_target
line_radius ss_helix_psi_exclude
[[line_smooth]] ss_helix_psi_include
line_stick_helper ss_helix_psi_target
line_width ss_strand_phi_exclude
log_box_selections ss_strand_phi_include
log_conformations ss_strand_phi_target
logging ss_strand_psi_exclude
matrix_mode ss_strand_psi_include
max_threads ss_strand_psi_target
max_triangles state
[[mesh_color]] static_singletons
[[mesh_lighting]] [[stereo]]
[[mesh_mode]] [[stereo_angle]]
mesh_normals stereo_double_pump_mono
[[mesh_quality]] [[stereo_mode]]
mesh_radius stereo_shift
mesh_solvent [[stick_ball]]
[[mesh_type]] [[stick_ball_ratio]]
[[mesh_width]] [[stick_color]]
[[min_mesh_spacing]] stick_fixed_radius
mouse_limit [[stick_nub]]
mouse_restart_movie_delay stick_overlap
mouse_scale stick_quality
mouse_selection_mode stick_radius
movie_delay [[stick_transparency]]
movie_loop stick_valence_scale
multiplex stop_on_exceptions
no_idle surface_best
nonbonded_size surface_carve_cutoff
normal_workaround surface_carve_selection
normalize_ccp4_maps surface_carve_state
normalize_grd_maps surface_circumscribe
normalize_o_maps surface_clear_cutoff
nvidia_bugs surface_clear_selection
opaque_background surface_clear_state
[[orthoscopic]] surface_color
overlay surface_debug
overlay_lines surface_miserable
pdb_conect_all [[surface_mode]]
pdb_discrete_chains surface_normal
pdb_echo_tags surface_optimize_subsets
pdb_hetatm_sort surface_poor
pdb_honor_model_number surface_proximity
pdb_insertions_go_first surface_quality
pdb_insure_orthogonal surface_ramp_above_mode
pdb_literal_names surface_solvent
pdb_no_end_record surface_trim_cutoff
pdb_reformat_names_mode surface_trim_factor
[[pdb_retain_ids]] surface_type
pdb_standard_order suspend_updates
pdb_truncate_residue_name swap_dsn6_bytes
pdb_unbond_cations sweep_angle
pdb_use_ter_records sweep_mode
[[pickable]] sweep_phase
png_file_gamma sweep_speed
png_screen_gamma test1
power test2
pqr_no_chain_id text
presentation texture_fonts
presentation_auto_quit [[transparency]]
presentation_auto_start transparency_mode
presentation_mode transparency_picking_mode
preserve_chempy_ids triangle_max_passes
pymol_space_max_blue trim_dots
pymol_space_max_green [[two_sided_lighting]]
pymol_space_max_red use_display_lists
pymol_space_min_factor [[valence]]
raise_exceptions valence_default
rank_assisted_sorts valence_size
ray_blend_blue validate_object_names
ray_blend_colors [[virtual_trackball]]
ray_blend_green wildcard
ray_blend_red wizard_prompt_mode
ray_color_ramps wrap_output

[[Category:Settings|All Settings]]

APBS

2007-01-20T23:48:33Z

Martoss: /* Installing the Dependencies on Linux */

== Introduction ==
[[Image:Rna_surface_apbs.png|thumb|APBS-generated electrostatic surface displayed in PyMOL]]
[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.

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.

'''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.'''

==Required Dependencies==
[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.

----
===Installing the Dependencies on OS X===
#First, [http://agave.wustl.edu/apbs/download/ register] your use of the software. This will keep everyone happy.
#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.
#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

fink self-update
fink install apbs

or if you want to use the multi-processor version, issue

fink self-update
fink install apbs

Then install the X-windows based version of pymol using the command

fink install pymol-py24

Note that the fink version of pymol '''already has''' the latest version of the APBS plugin. You are set to go!

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].

----

===Installing the Dependencies on Linux===

====RPMs====

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.

====Debian packages====

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

sudo dpkg -i apbs*.deb

====Gentoo====

You have to install apbs and pdb2pqr. Both are masked via keywords atm. Type as root:

echo sci-chemistry/pdb2pqr >> /etc/portage/packages.keywords

echo sci-chemistry/apbs >> /etc/portage/packages.keywords

emerge -av sci-chemistry/apbs sci-chemistry/pdb2pqr

----

==Further contributions and edits are needed.==