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ChangeLog
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=========================================================================
CHANGE LOG
=========================================================================
2013-09-09 Thomas Holder
* add "x" "y" "z" selection operators
Example: select foo, x < 12.3
2013-09-08 Blaine Bell, Thomas Holder
* fix seq viewer background color
* add "backbone" and "sidechain" selection keywords
* fix: cealign inverts target structure
2013-08-27 Thomas Holder <[email protected]>
* fix [bugs:#135] array overrun
https://sourceforge.net/p/pymol/bugs/135/
* apply one part of [patches:#6]
https://sourceforge.net/p/pymol/patches/6/
* preserve "use_shaders" setting when loading session files
* simplify pymolrc search routine
* fix CtSh-M click on group members in object menu panel
* set_key string support
2013-08-13 Thomas Holder <[email protected]>
* fix h_add atom sorting
* add "metals" keyword to selection language
2013-07-31 Thomas Holder <[email protected]>
* improve amber rst/crd support
* fix pair_fitting with one atom pair
2013-07-23 Thomas Holder <[email protected]>
* fix numpy/ndarrayobject.h import
* setup.py: add --osx-frameworks agument
* rpc server: use register_instance
2013-07-16 Thomas Holder <[email protected]>
* fixed load_traj with stop/max arguments.
Thanks to David Osguthorpe for the patch.
* fix pymol.importing.read_mmodstr
* proper numpy support (ObjectMap.c)
* take out broken experimenting.expfit
* fetch_path: graceful error handling when writing file fails
2013-07-15 Blaine Bell <[email protected]>
* fixed flickering ortho problems on some machines
2013-06-21 Blaine Bell <[email protected]>
* fixed selection indicators
2013-06-18 Blaine Bell, Thomas Holder
* fixed loading in bg_rgb settings from old project pse files
* add URL support for run command
2013-06-13 Blaine Bell <[email protected]>
* fixed labels when use_shaders is 0 and show_frame_rate is on
2013-06-12 Thomas Holder <[email protected]>
* update APBS Tools plugin
* fix spectrumany when minimum/maximum are provided
2013-06-11 Blaine Bell <[email protected]>
* Open Source PyMOL v1.6.0.0
* freeing VBOs properly when deleting volumes
* added quiet flag for SettingGenerateSideEffects() and SettingCheckUseShaders()
* fix 15bit color picking
* fix surface memory leak
* fix CGO demo
2013-06-10 Thomas Holder <[email protected]>
* internal.file_read: use urllib2 instead of urllib
* fix ellipsoid transparency OpenGL rendering
2013-05-27 Thomas Holder, Blaine Bell
* fix surface normals
* fix Scripts ending with ...pymol.py do not execute
https://sourceforge.net/p/pymol/bugs/46/
* several CGO fixes
* several python fixes
2013-04-26 Thomas Holder <[email protected]>
* refactored importing.fetch
* spectrum enhancements (arbitrary expressions and colors)
* pymol2.cmd2: implement proxy pattern
* chempy model improvements
* fix bg_color, which sometimes did not apply instantly
2013-04-17 Thomas Holder <[email protected]>
* support full path for "matrix" argument
https://sourceforge.net/p/pymol/patches/4/
* use PyMOL API in pymol.rpc module
https://sourceforge.net/p/pymol/patches/3/
* doc string for cmd.find_pairs
https://sourceforge.net/p/pymol/patches/2/
2013-04-12 Blaine Bell <[email protected]>, Thomas Holder <[email protected]>
* rotate ANISOU vector when transforming objects
* new command: split_chains
* fix create/extract bug with movie
* fixed cartoon VBO memory leak
* always draw rounded caps with sticks shaders
* several shader fixes and performance improvements
* fixed screen z-offset for labels
2013-03-22 Blaine Bell <[email protected]>, Thomas Holder <[email protected]>
* improved rendering performance using shaders, including
dynamically updated shaders based on settings
(see data/shaders directory)
* implemented shaders for menus, labels, selection indicators,
background, and other graphics that were not using shaders.
* consolidated textures used for labels and selection indicators
to one texture, which helps performance
* added memory checking to help avoid crashing when memory is
low or not available
* cleaned up code base, took out extraneous preprocessor code and
code that was not used.
* refactor pmg_tk.Settings
* Do not clear atom names with chempy.champ.assign.amber99
* fix some plugin manager exception handling
* fix create with name=None
* Plugin override search path: Always include "startup"
from installation directory in plugin search path
* Movie > Program > Scene Loop > Nutate > by degrees
* ObjectMeshRenderImpl refactoring: color isomesh and isodot with
mesh_color and dot_color settings
* merging alignment objects: eliminate orphaned atoms
* fix cealign alignment object creation: rms_cur arguments swapped
* improved the alignto command to take additional keyword arguments
which get passed to the used method -> object=aln supported now
* remove _PYMOL_MODULE constant
* fix LITERAL mode command parsing: ignore leading whitespace
2013-02-14 Thomas Holder <[email protected]>
* enable VMD plugins by default
* apply patch #120 "pymol" import in launcher ambiguous
http://sourceforge.net/p/pymol/bugs/120/
* always import _cmd from pymol or pymol.cmd instead of relative
* add bz2 support for reading PDB and some other file formats
* support width/height units with the png command
* support decorator syntax for cmd.extend
* setup.py refactoring, setup2.py no longer needed
2013-01-10 Thomas Holder <[email protected]>
* Exit on error with "-y" flag
* shortcut and auto-completion refactoring
* fix setting angle_color or dihedral_color
* ramp_new: exception handling on argument parsing
2012-12-07 Thomas Holder <[email protected]>
* feedback fixes
* speed up iterate and alter - https://sourceforge.net/p/pymol/patches/5/
* command line (Tk GUI) history improvements
* add angles to the Movie-Program-SceneLoop menu
* Fixed fab hydro argument
2012-11-12 Thomas Holder <[email protected]>
* Fixed #3539436: right justified resn in PDB
* Fixed #3506103: alignment objects from "super" do not contain N atoms
* Fixed #3496006: END before ENDMDL bug reintroduced
2012-08-15 Jason Vertrees <[email protected]>
* Fixed longstanding annoyance: 'as rep, vis' now works
2012-08-14 Jason Vertrees <[email protected]>
* Added autocomplete for 'group' command.
2012-08-14 Jason Vertrees <[email protected]>
* Adding autocomplete for 'dss'.
2012-08-14 Jason Vertrees <[email protected]>
* Fixed bug where FASTA strings aren't returned for multiple objects.
2012-06-06 Jason Vertrees <[email protected]>
* Fixing up CEAlign (thanks to Thomas Holder)
* FIXED: fails to align chains of length < 2*window+1
* FIXED: if chain length is a multiple of window, only (length-window) residues get aligned
* FIXED: only evaluates every 2nd path of the best 20 (increments k twice in the loop)
* FIXED: if no alignment is found, the return value is NULL which raises a SystemError instead of a graceful error message.
* FIXED: finally, it's not possible to obtain the alignment as an object (like with align ..., object=aln)
* FIXED: fixed auto complete names on for cealign
2012-05-30 Blaine Bell <[email protected]>
* Fixing the exception handling of get_names_of_type
2012-05-30 Jason Vertrees <[email protected]>
* Fixing get_unused_names
* Fixing locking on get_names_of_type
2012-04-06 Jason Vertrees <[email protected]>
* Adding checks for Quadro cards to enable cylinder shader workaround.
2012-04-06 Jason Vertrees <[email protected]>
* Improved PyMOL Plugin System; Thomas Holder's PyMOL OSFP project
2012-04-06 Jason Vertrees <[email protected]>
* Standard splash
2012-04-05 Jason Vertrees <[email protected]>
* Default all Intel cards to not use shaders
* Fixed ID:3513708, cmd.get_unused_name fix; thanks to Thomas Holder
* Added new splash image for open-source build
2012-03-20 Jason Vertrees <[email protected]>
* Fixed ID: 3512313 TER records before residues like MSE, patch submitted by Thomas Holder
2012-03-05 Jason Vertrees <[email protected]>
* fixed crash when reading in long lines from stdin
2012-03-03 Jason Vertrees <[email protected]>
* updating version 1.5.0.2 -> 1.5.0.3
* fixed error showing Cell on map with attached file
* fixed reading in symmetry
* fixed problem with symmetry copying/setting where map doesn't get updated
* get_symmetry should return None if argument is not an ObjectMolecule or ObjectMap
* stack trace when hiding everything for mesh
* fixed Volume extents only get shown when volume is rendered
* fixed copying Symmetry info into Objects (ObjectMap and ObjectMolecule)
* fixed reading in legacy sessions with version # less than 1
2012-02-17 Jason Vertrees <[email protected]>
* Fink/Macport builds fixed; thanks to Jack Howarth for the patch.
2012-02-17 Jason Vertrees <[email protected]>
* Open Source PyMOL v1.5.0.2
* stack trace when saving movie as MPEG (ID: 3488608)
* error loading from pse that don't have Crystal/Symmetry info
(ID: 3488609)
2012-02-13 Jason Vertrees <[email protected]>
* adding necessary files to build PyMOL v1.5.0.1
2012-02-13 Jason Vertrees <[email protected]>
* Open Source PyMOL v1.5.0.1
* improved rendering Performance
* improved rendering Quality
* bg_gradient now ray traces
* improved cartoon support for non-standard nucleotides
* surface color smoothing
* surface-based picking
* frame buffer-based antialiasing for real-time rendering
* optimized anaglyph colors and intensities for an improved 3D
viewing experience
* real-time and ray-traceable ambient occlusion
* molecular weight calculuations; A > Compute > Molceular Weight
* selection generation A > Generate > Selection
* new mouse mode for repositioning lights
* many bug fixes
2012-01-03 Jason Vertrees <[email protected]>
* improved callback rendering
* improved cealign (thanks to Thomas Holder)
2011-12-16 Jason Vertrees <[email protected]>
* fixed object creation when merging two objects; thanks to James
Davidson for pointing out the error
2011-12-06 Jason Vertrees <[email protected]>
* fixed get_mass
2011-12-05 Jason Vertrees <[email protected]>
* fixed create to reorder IDs when combining objects; thanks to James
Davidson.
2011-12-05 Jason Vertrees <[email protected]>
* Cleaned up 'fitting.py' (untabified)
* alignto updated; can now take a method for alignment
* cealign updated; made faster and cleaner; thanks to Thomas
Holder for the ideas and patch
2011-10-05 Jason Vertrees <[email protected]>
* Added the get_viewport function and updated the viewport function
2011-10-05 Jason Vertrees <[email protected]>
* Added support for some non-standard nucleic acids (PSU)
2011-09-29 Jason Vertrees <[email protected]>
* Fixed distance invalidation problem
2011-09-19 Jason Vertrees <[email protected]>
* Added Display > Roving Detail
* Removed AttributeError on coloring volumes; needs better
solution though
* Added polar contacts/hydrogen bonds to the Measurement wizard
2011-09-19 Jason Vertrees <[email protected]>
* Doc fix
2011-09-16 Jason Vertrees <[email protected]>
* PyMOL now respects the h_bond_from_proton setting
2011-09-08 Jason Vertrees <[email protected]>
* Added A > Generate > Selection > polar, non_polar,
acceptor/donator options
2011-08-21 Jason Vertrees <[email protected]>
* Fixed click-flash that happens when middle-clicking when
showing the background gradient (thanks, Blaine)
* Added A > Compute > Molecular Weight and cleaned up the
compute menu in general
2011-08-15 Jason Vertrees <[email protected]>
* Fixed a conversion bug in util.cbc; thanks Hongbo.
2011-07-26 Jason Vertrees <[email protected]>
* one more fread
2011-07-26 Jason Vertrees <[email protected]>
* Fixing bugs introduced by last commit for freads; and fixed another importing bug
2011-07-25 Jason Vertrees <[email protected]>
* Fixing more warnings; opengl bindings work again; thanks to Jack
Haworth for the patch
2011-07-20 Jason Vertrees <[email protected]>
* Fixed lots of warnings on build; cleaning up code
2011-07-06 Jason Vertrees <[email protected]>
* Multi-model PDBs now write ENDMDL after models and END at end of file; thanks to Thomas Holder for the patch.
2011-06-23 Jason Vertrees <[email protected]>
* Code cleaning; reducing number of warnings
2011-06-22 Jason Vertrees <[email protected]>
* Small state bugfix
* Feedback bugfix
* Updated TNT to 3.0b
2011-06-16 Jason Vertrees <[email protected]>
* suppress guess valences warning message to Blather
2011-06-09 Jason Vertrees <[email protected]>
* fixed volume shader; esp for Ubuntu
2011-06-08 Jason Vertrees <[email protected]>
* "fix" for colored sticks problem
* fixed File > Save Molecule using object's state
* fog/shading in shaders
2011-05-18 Jason Vertrees <[email protected]>
* bugfix for drawing ribbons, drastically increases their rendering (3x+)
2011-05-18 Jason Vertrees <[email protected]>
* fixed a bug where group names were clipped
2011-05-18 Jason Vertrees <[email protected]>
* fixed state bug in distances for (all)
* fixed ray trace bug when not using Python
* fixed nucleic acid residue naming (Thanks to Thomas Holder)
2011-05-12 Jason Vertrees <[email protected]>
* more robust space group/pt group reading from maps
2011-05-02 Jason Vertrees <[email protected]>
* fixed state bug in distances for (all)
* fixed ray trace bug when not using Python
* fixed nucleic acid residue naming (Thanks to Thomas Holder)
2011-05-02 Jason Vertrees <[email protected]>
* fixed shader bug
* v1.4.1 release
2011-04-20 Jason Vertrees <[email protected]>
* finished the state counter
* all measures now work inter-distance, and
honor object states
* selecting/picking now works as we'd expect, with
respect to states
* improved shaders; added fog, fixed rendering issues
* bug fix for possible crash
2011-04-20 Jason Vertrees <[email protected]>
* freezing colors the states blue
* added out of bounds checks for showing states; those
beyond are shown as "--"
2011-04-20 Jason Vertrees <[email protected]>
* state_counter_mode
* fixed bg_gradient coloring
* added small dictionary for xray space groups
* get_names and safe names
2011-04-01 Jason Vertrees <[email protected]>
* transparent ribbons
* naive volume ray tracing; better version coming soon
* small bug fixes
2011-04-01 Jason Vertrees <[email protected]>
* introducing gradient backgrounds (non-ray tracing; testing)
* Windows bug fixes
* Rlight-click Volumes fix
2011-04-01 Jason Vertrees <[email protected]>
* PyMOL v1.4b1 -- adds volumes, glew, shaders, bug fixes, etc
2011-02-03 Jason Vertrees <[email protected]>
* Added PyMOL Web Services API; for information run
firefox pymol/modules/web/examples/index.html
2011-01-18 Jason Vertrees <[email protected]>
* Cygwin build fix (thanks Alex)
2011-01-18 Jason Vertrees <[email protected]>
* mol2 atom types
2011-01-11 Jason Vertrees <[email protected]>
* mol2 multi-state save bugfix
2011-01-11 Jason Vertrees <[email protected]>
* added mol2.py
* File->Save Moleulce
2011-01-11 Jason Vertrees <[email protected]>
* nascent mol2 writing
2011-01-11 Jason Vertrees <[email protected]>
* removed duplicate function; thanks Thomas
2011-01-03 Jason Vertrees <[email protected]>
* Fixed multi-state ray trace bug for CGO objects
2010-10-13 Jason Vertrees <[email protected]>
* Fixed Glutamine label problem in Residue menu; now ALT-Q.
2010-10-13 Jason Vertrees <[email protected]>
* Trajectory fix
2010-10-08 Jason Vertrees <[email protected]>
* charge wizard fix
2010-10-06 Jason Vertrees <[email protected]>
* memory fix on angles and dihedrals
* documentation update on cealign
2010-10-02 Jason Vertrees <[email protected]>
* Fully implemented dynamic measures; enable by turning on
"dynamic_measures"--disabled by default for testing
* Setting for surface residues
2010-10-02 Jason Vertrees <[email protected]>
* Measurement wizard dihedral fix
2010-09-23 Jason Vertrees <[email protected]>
* Fixed degenerate super bug.
2010-08-12 Jason Vertrees <[email protected]>
* Fixed the map fetching, again.
2010-08-12 Jason Vertrees <[email protected]>
* Added visibililty flag for Measurement Wizard
2010-08-11 Jason Vertrees <[email protected]>
* Fixed small bug with fetch.
* Moved surface area calculations to Compute > Surface area; these values still need to be validated!
* A > Action > Generate > Selection > Surface Residues
* New "surface_residue_cutoff" setting
* Removed one redundant option from Measurement wizard
* Added C > Color > Element > 6/H now colors by hydrogens, not carbons
* Yay for the new PyMOL website!
2010-08-05 Jason Vertrees <[email protected]>
* Better support for biological units.
2010-08-05 Jason Vertrees <[email protected]>
* For r1.3r1 (mostly due to fetch command)
* filtering on File > Save Molecule
* Mouse modes now tracked on measurement wizard
* Measurement wizard has surface area (beta!)
* typos
* fixed and cleaned up the fetch command
2010-05-28 Jason Vertrees <[email protected]>
* dynamic_measures setting, for dynamic distances
* more complete neighbor finding and concomitant settings:
- neighbor_cutoff
- polar_neighbor_cutoff
- heavy_neighbor cutoff
* versioning
* new (internal) build system
2010-03-24 Jason Vertrees <[email protected]>
* fixed a cealign bug
* added 'alignto' command back in
2010-03-24 Jason Vertrees <[email protected]>
* fetch_host setting (use 'pdb', 'pdbe', or 'pdbj')
* map fetching from EDS (eg. fetch 1cll, async=0; fetch 1cll, type=2fofc; fetch 1cll, type=fofc)
2010-02-18 Jason Vertrees <[email protected]>
* label_anchor setting
2010-02-16 Jason Vertrees <[email protected]>
* movie_quality setting
* copyright notices and install paths
2009-06-14 Warren L. DeLano <[email protected]>
* motions
2009-06-14 Warren L. DeLano <[email protected]>
* reduced Z scale sensitivity and added mouse_z_scale setting
2009-06-14 Warren L. DeLano <[email protected]>
* reindented source code using GNU indent for better readability
* ugly workarounds added for Radeon HD hardware -- warns user
2009-06-10 Warren L. DeLano <[email protected]>
* updated the density wizard to reflect the current API
2009-06-09 Warren L. DeLano <[email protected]>
* fixed rounding error bug with symmetry expansion of maps.
2009-05-18 Warren L. DeLano <[email protected]>
* pseudoatom labeling via main menu right-click
2009-05-13 Warren L. DeLano <[email protected]>
* fixed bug with names containing 'model' in selection macros
2009-05-11 Warren L. DeLano <[email protected]>
* experimental movie_panel setting
* changed internal_gui_mode=0 appearance again
2009-05-03 Warren L. DeLano <[email protected]>
* fixed internal_gui_mode, 1 and 2; added 2 rows to viewer window
* fixed bond color problem from maestro
* fixed 'ace' builder bug
2009-04-28 Warren L. DeLano <[email protected]>
* fixed ramp bug for transformed maps
2009-04-26 Warren L. DeLano <[email protected]>
* fixed bug with clicking on the sphere representation
2009-04-10 Warren L. DeLano <[email protected]>
* changed 'import pymol' behavior to defer launch until
finish_launching is actually called
* added warnings for pml/py/pym run/@ confusion
2009-04-09 Warren L. DeLano <[email protected]>
* added bycell selection operator
2009-03-26 Warren L. DeLano <[email protected]>
* acnt map support
* fixed bug with selection argument to cmd.get_names
2009-03-23 Warren L. DeLano <[email protected]>
* fixed problem unintentionally quashing "+" from filenames
* fixed selector bug parsing one+object as two + object
* added " + " selection operator to mitigate impact of bug
and added " - " operator to provide complement to " + "
2009-03-21 Warren L. DeLano <[email protected]>
* added simple fasta output
* fixed major bug with 'domain' argument to select
* greatly improved the performance of the peptide builder
* fab command
2009-03-20 Warren L. DeLano <[email protected]>
* very rough FASTA & ALN read support (full peptide builds)
2009-03-14 Warren L. DeLano <[email protected]>
* updated the vmd molfile plugin code from current UIUC cvs
* addressing various strict-aliasing issues for GCC
2009-03-13 Warren L. DeLano <[email protected]>
* field_of_view now interpolated via get_view/set_view matrix
(appears to be backwards & forwards compatible)
2009-03-11 Warren L. DeLano <[email protected]>
* front and back colors, label_color now defaults to front
* fixed object duplication deadlock bug
* show_frame_rate setting
* valence_mode=1 setting for nicer valence display
2009-03-10 Warren L. DeLano <[email protected]>
* dynamic_width settings and defaults
2009-03-06 Warren L. DeLano <[email protected]>
* addressed problem reading mmod files
2009-02-08 Warren L. DeLano <[email protected]>
* refactored multisave commmand
* improved read-in performance for concatenated PDB files
2009-02-08 Warren L. DeLano <[email protected]>
* fixed stupid load-from-URL bug...
* GZ compression support for common input formats
* confirmed DLP Stereo 3D support
* fixed ray-tracing for checkboard, byrow, & bycolumn stereo 3D
2009-02-06 Warren L. DeLano <[email protected]>
* saving .dat and .out now also default to mmod format
* extensive reworking of stereo 3D code to enable new encodings
2009-01-14 Warren L. DeLano <[email protected]>
* found & fixed longstanding issue with psize.py in APBS plugin
* eliminated alternative conformation identifiers from PQR files
2009-01-09 Warren L. DeLano <[email protected]>
* added PyMOL> prompt to the Tk Window
* addressed a couple of minor file saving issues
2009-01-05 Warren L. DeLano <[email protected]>
* removing old X11-hybrid kludge, fixed a few python issues
* default .mpg extension handling for MPEG export
2009-01-02 Warren L. DeLano <[email protected]>
* fixed click-through toggle for Leopard
2009-12-31 Warren L. DeLano <[email protected]>
* various changes associated with getting 1.2b0 out the door
2008-12-23 Warren L. DeLano <[email protected]>
* fixed tk-based session save problems reported by DB
2008-12-16 Warren L. DeLano <[email protected]>
* fixed another object-name-dragging bug
* mpeg1 export menu item
* fixed putty scaling bugs
2008-12-14 Warren L. DeLano <[email protected]>
* added support for writing ppm files (awkwardly: via png)
2008-12-13 Warren L. DeLano <[email protected]>
* added error message for when align/super atom alignment fails
2008-12-07 Warren L. DeLano <[email protected]>
* fixed split_states behavior to allow prefix to override titles
2008-12-07 Warren L. DeLano <[email protected]>
* updated pymol/__init__.py OpenGL autoconfiguration
2008-12-04 Warren L. DeLano <[email protected]>
* continued major overhaul of the builder
* fixed longstanding object name right-dragging bugs
2008-11-29 Warren L. DeLano <[email protected]>
* various updates to the builder
* auto_overlay setting
* stick_ball_color, stick_h_scale settings
* added support for negative stick_radius, stick_ball_ratio
2008-11-22 Warren L. DeLano <[email protected]>
* fixed incompatibility with Roche Pocket Viewer
2008-11-12 Warren L. DeLano <[email protected]>
* added max_ups setting to govern excessive geometry flux
2008-11-10 Warren L. DeLano <[email protected]>
* further work on the builder
* sculpting engine now respects atom flag 3 (fixed atoms)
2008-11-05 Warren L. DeLano <[email protected]>
* added Mac-only menu for configuring X11 click-through behavior
* updated open-source splash image
2008-10-04 Warren L. DeLano <[email protected]>
* first rough attempt at IDTF export for U3D / 3D-PDF support
2008-09-29 Warren L. DeLano <[email protected]>
* fixed subtle div-zero bug in the view interpolation code
2008-09-24 Warren L. DeLano <[email protected]>
* fixed crash bug with blank CGO object
2008-09-12
* added menu option & mechanism for removing plugins