Changes Under Consideration
NOTE: Some of these are mutually exclusive, and many of them will
never be carried out -- they are listed here so that I don't forget
about them and so that you can see ways in which core PyMOL might
evolve.
* Allow multiple, parallel transformation matrices for each object
* Create a Rasmol translator in Python
* IO routine for a generic volume data object (to supplement bricks and maps)
* Support mapping of additional dimensions into volume data sets
for use in coloring all PyMOL geometries according to electrostatic
potential and the like.
* "Fragment" wizard, tied into the fragments subsystem.
* "Batchmin" wizard ?
* Real Edit Menu in Tk
* CTRL and CTRL/SHIFT numbers should add aromatic and aliphatic
ring systems in the builder respectively within the molecular editor.
* support anisotropic B-factor renditions (ellipsoids)
* support reading and writing of XPLOR PSF/PDB files to enable direct
use of NAMD with PyMOL. Note that this will require integration of
basic force-field structures into PyMOL...not a lightweight task, but
something I think should be done in a general way to facilitate
use of PyMOL as a molecular modeling tool...
* support direct reading of DCD, Amber, and/or Gromacs trajectory files
* support output of Amber input files so that we can bypass xleap altogether
* support MOL2 and multi-MOL2 file formats
* fold MMTK into the main PyMOL distribution, and merge the two programs in a way
which allow the user to "see" into MMTK's internal data structures using
PyMOL while calculations are being performed.
* create a VRML->CGO converter so that VRML can be displayed inside of PyMOL
* create a VRML writer to facilitate export of PyMOL geometries.
* support CML via some "swallowable" python XML parser
* add in support for CGL's annotated PDB file format
* make PyMOL a compliant extension for the Chimera environment
* add a dynamic 3-D based tutorial
* finish abstracting GLUT away from PyMOL and wrap it inside of TOGL so that
Chimera and PyMOL can share a context
Specific Requests from Users
* Get label support into the raytracer (build a 3D character set)
* Enable specific xyz positioning of labels (w/ mouse?)
* Cutting of images to the MS Window's clipboard for easy pasting into Powerpoint
Current and Ongoing Goals
* make an ActiveX control which contains the core PyMOL viewer for
use in web browsers and many other crazy contexts.
* clean up return values in the API and qualify exceptions. Include the source
module name in messages, and provide proper feedback conditionals
* update 'expand' and 'attach' to take an atom name as well as an element symbol
* complete first-round test-cases.
* complete matrix-based object translation and rotation
* place feedback conditionals around all error output.
* create alter_state_atom command (combine PAlter and PAlterState into one function)
Main Goals for 1.0 Release
* Side-by-side stereo support: cross-eye and wall-eye
* MOL2 and CML file formats
* Generalized volumetric rendering: (1) mesh (2) solid (3) colormaps
* Integrated tutorial/demonstration system
* Fully consistent API (defined and correct return values)
* Complete GLUT independence (internal character sets)
* Basic building support for biological polymers & small molecules
with and w/o hydrogens
Current Bugs to Fix
* superposition system fails with degenerate sets (planer systems, etc).
sometimes it just fails period
Changes up to 0.82
* modified "cmd.system" to take an argument for asynchronous execution
* flag command no longer indicates atoms by default -- set "auto_indicate_flags"
* cross-eye side-by-side stereo support
* fixed bug in valency display code
* fixed major bug in "create"
* raytracing bugfix for bond with zero length
* complicated workaround for mouse atom selections with Radeon 8500 and WinXP
PyMOL may now be somewhat resistant to broken OpenGL ReadPixels implementations
* improved water handling for "non-canonical" situations (i.e. real life muck)
* moved configuration files to a subdirectory "setup"
* mpng now can support a range in order to enable coarse-grained parallelism
(distributed movie rendering)
* "within" operator added to selection language
* visible selection operator no longer hits disabled objects
* origin, zoom, and orient now take "state" as optional argument with special
handling for 0 (all states) and -1 (current state)
* eigensolve output now considered blather
* important bug-fix on rotate and translate commands
* "present" operator in selection language and tests for "state" operator
Changes up to 0.81
* fixed bug in bg_color API function
Changes up to 0.80
* major bug fix to "carve" in isomesh
* "command ?" now gives a list of arguments
* fix spurious bugs reading files under unix
* added support for alternate residue id codes in secondary structure records
* cylinders have become sausages, and...
...we now have flat-capped cylinders (0203)!
* fixed duplicate logging with Run command
* create a simple vector-based font (0203)
* 3D text in CGOs
* linear constraints in molecular sculpting engine
* acetylene buidling block
Changes up to 0.79
* internal character set
* solid isosurface rendering algorithm: "isosurface" command
* parser updated to handle selections like "resi 10 and (name c,n,o) and chain A"
which lack surrounding parentheses, but which have delimiters inside
* parser updated to handle (alt A+'') and similar constructs (previously DOA).
* fixed ribbon & cartoon display when N-terminal atom is the CA
* changes to support MacOSX port (0203)
* ALIGN command
Changes up to 0.78
* revamped Makefiles for better portability and dependency handling.
Changes up to 0.77
* sculpting information now cached between changes to molecular structures
* optimized sculpting for small regions of large proteins
* FINALLY, modes for two-button mice
Changes up to 0.76
* VDW radii adjusted. Use "set legacy_vdw_radii=1" on start-up for old values.
* Sculpt functionality. Who needs gummy bears when you can have gummy molecules?
* Numerous back-end bugs addressed.
* transparent spheres
Changes up to 0.75
* enabled automatic completion in the tcl/tk command window
* altered settings for dot representation
* created stop_on_exception and raise_exceptions settings.
WARNING: stop_on_exceptions is NOT set by default (this is so that
log files which contain errors will continue to function).
* gutted cmd.py, and created a bunch of sub-modules which contain the
code previously in cmd.py.
* superposition bugs fixed with multi-state objects (fit and intra_fit)
* cmd.set_key can now be used to redefine ALT and CTRL keys in addition
to function keys and other specials.
Changes up to 0.74
* very minor bug/doc fixes
Changes up to 0.73
* improved fragment and residue building capabilities
Changes up to 0.72
* fixed some logging issues with dragging pieces
* now possible to create empty objects, fixed mutagenesis wizard in response
* all readable files are shown by default in the Tkinter file dialogs.
Changes up to 0.71
* seg. fault bug fix in ObjectMoleculeConnect
* two_sided_lighting option to help Jun at CCI project
* fixed triangle rendering on lower-end graphics cards
* revamped PyMOL's internal bond handling data structure. I've done my best
to insure that this doesn't break anything, but it is a major change
and has the potential to create huge problems...
* empirically synchronized PyMOL and PovRay's perspective transformations...
Changes up to 0.70
* fixed symmetry bug with multiple state objects
* symmetry now carried through create operations
Changes up to 0.69
* PNG reading
* First generation PovRay interface...whoopee!
* Tweaked util.ray_shadow and added some new settings
Changes up to 0.68
* HETATMS are no longer surfaced by default. Clear the "ignore" flag or
set surface_mode=1 to restore their surfaces.
* flag command now takes name arguments and can now reset, set, and clear
flags
* established some standard flag names and conventions
* Upgrading OpenGL Pop-up menus, since it looks like the internal GUI
will be widely used despite its original limited role (oh well...)
* Fixed element name guessing
* added ray_improve_shadows setting for improving shadows by
projecting outward from triangles.
* Fixed a major bug in the raytracer which was causing bogus shadows to appear
on surfaces
* Fixed a huge bug in surfacing of subsets. That function was totally whacked,
but no one had noticed or complained!!! Revised the function of the
surface_proximity setting
* by default, PDB HETATMs are no longer surfaced -- if you want them to be, then
please "set surface_mode=1"
* "transparent" renamed to "transparency"
* switched to a three-pass OpenGL rendering model in order to properly display opaque,
transparent, and antialiased objects
* OpenGL transparency now works too! See "help transparency".
* nonbonded spheres are now pickable
* surface_color and mesh_color override the default atom colors
for uniform surface coloring -- added support for color names
into the settings module
* flags 24 and 25 now work with surfaces and meshes. See "help flags"
Changes up to 0.67
* Transparency support in rendering has been added, but it doesn't yet
exist yet in opengl mode.
Changes up to 0.66
* numerous bug-fixes
Changes up to 0.65
* numerous bug-fixes
Changes up to 0.64
* stage 1 API enhancements -- consistent return conventions adopted
(many will not follow conventions until stage 2 though)
* more surface_qualities: -3 to 2, surface_quality=1 is now even better
* click-and-drag a box to select atoms
* PyMOL now builds w/o warning in VC++6
* LOG FILE CAPABILITIES: logging of both PyMOL scripts (.pml) and
PyMOL program files (.pym). The "resume" command allows propagation
of session-like behavior. This makes a huge difference in PyMOL
user-friendliness.
* autocompletion bug fixed, generalized autocompletion added
* mesh_radius cut in half, for better default density figures
* carve command on isomesh
* pymolrc support
* isosurface speed boosted by about 33% using C-oriented field object.
* fixed bugs with internal_gui options
* internal_feedback setting
* simple cartoon ribbon for DNA/RNA
* selection language now supports '+' as substitute for commas, and '-'
as substitute for ':' in residue identifiers (more user friendly)
* selections no longer require parentheses unless they have commas or
semicolons
* unit cell display for molecules and meshes
Changes up to 0.63
* Density wizard
* isomesh meshes now use mesh_width instead of line_width
* fixed rendering background color bug on BigEndian machines
* fixed fatal bug with symexp
* first attempt at support for CCP4's binary maps -- it works with my
test maps, but will it work with others?
Changes up to 0.62
* tuned up the util.ray_shadows function, added a "matte" mode for better
definition of ribbons...
* integrated workaround for an apparent GCC serial optimizer bug on x86.
Changes up to 0.61
* bg_color command for easier background adjustments...
* depth cue menu item and ray_trace_fog linked
* cartoon_discrete_colors hack for coloring secondary structure properly
* (ss ...) primitive in selector for selecting helices, etc.
* many cartoon ribbons improvements -- flat fancy sheets now VERY nice.
Changes up to 0.60
* third generation fancy helices complete -- revamped interpolation code.
* ray now takes dimensions for rendering larger than screen
* unpick and hide selection buttons
* various new menu items...
* preparing for GLUT independence on selected platforms...
* choice of lighting modes for ray-tracing (improved shadows, contrast)
* settings renames (gl_ambient, dot_radius)
* settings changes (hash_max) and ray-tracing feedback
* "help faster"
* fixed minor glitch with fancy helices
Changes up to 0.59
* fixed valency display bug...
Changes up to 0.58
* second generation cartoon ribbons are in -- Goodbye Molscript!
* fixed half-decade old logic bug in MemoryDebug (blush!).
* "alter" and "alter_state" given a 50% performance boost
* added a coarse hydrogen-bond assessment feature (internal)
* added phi/psi measuring capability
* fixed selector memory leak on errors
* added first-generation cartoon riboons
(higher-quality to come later)
* added more specific settings for mesh and ribbon width, etc.
* add more settings-change side-effects
* fix bugs with saving pkl files for state > 1
* added a concise notation into the selection language
model/segment/chain/residue/name
*/name
residue/
residue/name
chain/ /
chain/residue/
chain/ /name
chain/residue/name
segment/ /
segment/ / /name
segment/ /residue
segment/ /residue/name
segment/chain/ /
segment/chain/ /name
segment/chain/residue/
segment/chain/residue/name
/model
/model/ / / /name
/model/ / /residue
/model/ / /residue/name
/model/ /chain
/model/ /chain/ /name
/model/ /chain/residue
/model/ /chain/residue/name
/model/segment
/model/segment/ / /name
/model/segment/ /residue
/model/segment/ /residue/name
/model/segment/chain
/model/segment/chain/ /name
/model/segment/chain/residue
Changes up to 0.57
* mutagenesis module
* finished the set_dihedral command
Changes up to 0.56
* fixed a serious parser bug with the mdo command
Changes up to 0.55
* fixed and enhanced util.mroll, util.mrock
Changes up to 0.54
* ID and elem fields in alter, iterate
Changes up to 0.53
* change order of drawing within object to improve the
interaction with antialiased lines.
* thread safety improvements (fixed bug involving serial
manipulations of the same object)
* bug fix with stick representations
* fixed minor goof with cmd.dist retval in 0.52
Changes up to 0.52
* many improvements to online help
* fixed discrete objects created from PDB files
* prevented deadlock condition with re-entrant API locks
* fixed couple of logic-bugs in threading
* changed output format from mouse click to a valid selection
* finished retrofit of the parser.
* formal charge now read from MOL files -- need to consider full
implementation of MOL file reading capability (incl stereo)
Changes up to 0.51
* Tcl/Tk GUI now contains a save molecule option
* Tcl/Tk GUI help improved
* performance/quality options in the display menu
* sphere quality setting
* depth_cue toggle setting (important for low-end PC hardware)
* specular reflections
* fog setting
Changes up to 0.50
* can now "pick" C-alphas in the ribbon
* can now "pick" atoms and bonds in the stick representation
* improved clipping plane control command "clip"
* pym file extension support, for PyMOL-specific .py files
* better windows NT compatibility
* settings browser
* view, view_get, view_set commands
* Parser now contains a general shortcut handling module to
further help in reducing typing
* Slight tweak of the virtual trackball
* Saving and restoring matrix, center, origin, zoom, clip
* Internal program output no longer includes python's stderr
* New thread management solution -- simple and stable -- plus
it even works (I've even got test cases to prove it)!
* Fixed memory-trashing bug in the selector
* Found a workaround for KDE/Gnome/Tkinter/Tcl/Tk problems under linux
* Created Save option on the Tkinter menu, and added additional file types.
* TAB-activated filename and command completion (CTRL-D too)
* Former TAB functionality moved to ESC (text/graphics toggle)
* Auto-detection of stereo capability
* Created a robust Feedback control mechanism
* Eliminated hangs and crashes upon program termination with Win2k/NT.
* "Distances" wizard (internal gui;replace with external version later)
* "Pair Fit" wizard (internal gui; replace with external version later)
* Mesh objects now have states, and new meshes are appended.
* Modified raytrace antialiasing transfer function to improve sharpness.
* Created alias and extend commands so that python scripts can extend the
pymol language on the fly.
* Additional test cases.
* Parser improved with a new argument parsing subsystem which has a
better mapping to standard Python arguments. This has significant
potential to break existing code if there are any bugs, but I am
shooting for 100% backwards compatibility.
Changes up to 0.49
* Improved editor, hydrogens now auto-deleted.
* Visible selections.
* Default mouse actions changed for editing and atom selecting.
* Callback objects (for use with PyOpenGL) now have extents.
* get_state and get_frame API functions
Important Changes 0.42-0.48
Too numerous to list them all...
* Addition of support for PyOpenGL-based GL calls with callback objects
* Wizard feature, for grabbing mouse input -- still needs flushing out.
