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ChangeLog
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ChangeLog
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=========================================================================
CHANGE LOG
=========================================================================
2024-04-09 Jarrett Johnson, Thomas Stewart, Thomas Holder, Anton Butsev
* 3.0.0
* Panels
- Nucleic Acid Builder supported
- Scenes Panel (Basic version)
- Improved APBS electrostatics plugin integrated
* Distance/Bonding detection
- Halogen-bond detection and display
* Python API
- `fnab` command (sequence to nucleic acid chain)
- Improved CGO builder API
- get_sasa_relative() `subsele` argument added
- new clip modes/API
- iterate() adds `explicit_valence` and `explicit_degree`
- `cell_centered` setting added
- by grid-cell background gradient `bg_gradient=2`
- look_at() added
- experimental `curve_new` / `move_on_curve`
* Developer
- C++17 required
- pymol-testing integrated
- pytest introduced
- Github Actions CI
* And many other fixes and small additions provided by developers
and the community...
2021-05-10 Jarrett Johnson, Thomas Holder, Thomas Stewart
* 2.5.0
* File Import/Export
- DX binary map import (*dxbin)
- PDB/MMTF export: symmetry information now added
- Improved FASTA import
- Support for map.gz and mrc.gz extensions
* Builder & Panels
- Improved Fuse command (disallows hypervalent bonds, substitute monovalent atoms instead of attaching to them)
- Customizable keyboard shortcut menu
- Properties inspector now supports unsetting settings with “Delete” key
* Graphics & Visualization
- Ray interior colors now match primitives with `set ray_interior_color, atomic`
- Isomesh transparency support
- `sphere_mode` 5 removed (9 as replacement)
- Curved cartoon cylindrical helices
- Isosurface generation via marching cubes with setting `isosurface_algorithm, (0, 1)` (0 requires VTKm)
* PBC Handling
- Periodic boundary conditions supported in rebond, smooth, and intra_fit
* Python API
- Python 2 support removed
- pbc argument added to rebond, smooth, and intra_fit
- png(None) returns bytes
- scene_order() allows list for `names`
- pbc_wrap() and pbc_unwrap added
- matrix_reset() supports `state=0` for all states
- editing_ring() added
- unset now restores the default value for global settings
- load_traj now uses state=1 by default
- get_area command and dots representation: Exclude “flag ignore” atoms
2020-05-20 Thomas Holder, Jarrett Johnson
* 2.4.0
* load_traj
- support netcdf format
- support `selection` argument with all file formats
* CCP4/MRC Map Support
- Distinguish .ccp4 and .mrc extensions (regarding origin)
- .map extension: auto-detect the format
* New distance mode 8
* MMTF export: Consider `pdb_retain_ids` setting
* GLTF export (based on collada2gltf)
* New `internal_gui_name_color_mode` setting
* MPEG4 Movie export: Apply `movie_fps` setting to exported file
* Python API
- Improved error handling with exceptions
- New: cmd.rebond()
- New: cmd.get_capabilities()
- Fix: cmd.get_bonds() state off by one
- cmd.fit() et al.: raise on error
* Launch Options
- Restore `-V` launch argument for external GUI height
- macOS: `open` event opens new window
2019-02-11 Thomas Holder, Jarrett Johnson
* 2.3.0
* atom-level cartoon_transparency
* aln export for Nucleic Acids
* new API function: cmd.set_raw_alignment()
* fetch async=0 by default
2018-08-16 Thomas Holder, Jarrett Johnson
* fast MMTF export (requires mmtf-cpp)
* new setting: seq_view_gap_mode
* 2.3.0a0 (unstable/experimental)
2018-07-24 Thomas Holder, Jarrett Johnson
* 2.2.0
* Wizard > Mutagenesis > Nucleic Acids
* load format "pqr": retain_order=1
2018-07-03 Thomas Holder, Blaine Bell, Gabriel Marques
* Graphics refactoring, ported from Incentive PyMOL
Ported features:
- label improvements (multiline, connectors, background color)
- transparency_mode 3: Order-independent transparency
- bg_image_filename: Background image support
* new dependency (header-only): glm
2018-06-08 Thomas Holder <thomas.holder@schrodinger.com>
* fix selection wildcard (sf.net/p/pymol/bugs/209)
* fix PDB atom id > 99999 crash
* more robust PQR parsing
* pymol2.PyMOL() context manager
* new setting: cif_metalc_as_zero_order_bonds
* new setting: sdf_write_zero_order_bonds
* cif: accept _chem_comp_bond.type alias for _chem_comp_bond.value_order
2018-05-03 Thomas Holder <thomas.holder@schrodinger.com>
* fix anaglyph stereo in batch (headless) mode
* fix possible memory corruption with boolean settings
* measurement wizard: distances between states (all_states=on)
* get_fastastr: nucleic acid, by chain
* menu: A (Action) > group
* sequence viewer menu: ss (Secondary Structure)
* MAE export of groups (s_m_subgroupid)
* macOS: -O3 -fno-strict-aliasing (bugs/205)
2018-04-10 Thomas Holder <thomas.holder@schrodinger.com>
* sf.net/p/pymol/bugs/199 bash -> sh
* ignore zero-order bonds in neighbor lookup, this could cause
wrong bond order guessing in distance based bonding
* fix crash loading reduced 5ijo.mmtf
* volume panel: fix zoom (CTRL+R-Drag) and value input (R-Click)
* QOpenGLWidget support (not active by default)
* --gldebug -> backtrace on GL error
* 2.2.0a0 (unstable/experimental)
2018-03-13 Thomas Holder <thomas.holder@schrodinger.com>
* 2.1.0
* PyQt interface
2018-02-28 Thomas Holder <thomas.holder@schrodinger.com>
* stick_round_nub for COLLADA export
* UTF-8 in feedback
* display_scale_factor (ported from Incentive PyMOL)
* dx map import: support "type float" and skewed delta
2018-02-07 Thomas Holder <thomas.holder@schrodinger.com>
* new selection keywords: polymer.protein polymer.nucleic
* new command: multifilesave
* MMTF export (requires simplemmtf python module)
* select: present, state -1 -> current object state
* create: source_state = -1 -> current
(was: source_state = -1/0 -> all)
* cif: support quoted '?' and '.' as values
cif_get_array -> None instead of empty string for ? and .
* fix copy discrete object w/o coords
* fix loading pdbqr AutoDock 4 atom types
* fix get_model('none') and get_str('mol', 'none')
* h_add refactored: 5x faster, support discrete objects
2017-12-21 Thomas Holder, Piotr Rotkiewicz
* Python 3.7 support (https://sf.net/p/pymol/bugs/197/)
* enable align with alt-codes
- allow matching of non-alt-code to alt-code atoms in alignments
- swap sorting priority of 'name' and 'alt' identifiers
- sort empty 'alt' before non-empty 'alt'
* flags 6 and 7 for protein and nucleic acid
* mmCIF: read _atom_site.pdbx_formal_charge
* improve coordinate loading from mmcif chem_comp files
- ignore columns with all ? (missing) values
- select columns with "chem_comp_cartn_use" setting
* fix h_add: skip missing coordinates
2017-12-05 Thomas Holder, Piotr Rotkiewicz
* Python API: New "auto library mode". Automatically start a
non-GUI PyMOL instance if the pymol.cmd API is used without
running pymol.launch() first
* pdb_echo_tags for mmCIF and MMTF
* command parser: improve exception handling
* fix some PSE export memory leaks
* pymol2.cmd2: eliminate (non-weak) circular references
* movie making: reinterpolate after add_nutate/add_roll etc.
* support "module:callable" in loadfunctions/safefunctions
* yellow state indicator for discrete objects
* mpng modal draw improvements
2017-10-23 Thomas Holder <thomas.holder@schrodinger.com>
* pse_export_version support with Python 3 (experimental)
* fix setup.py --use-msgpackc=guess: catch EnvironmentError
2017-10-18 Thomas Holder <thomas.holder@schrodinger.com>
* 1.9.0.0
* use PyMOL 2.0 setting defaults
* L > residues (oneletter)
* fix py3 crash in "A > copy to object"
* fix scene object visibility with hidden groups
* fix "ending" after loading movie session
2017-09-13 Thomas Holder, Piotr Rotkiewicz
* expose "oneletter" to label/iterate
* sequence viewer: MSE=M SEC=U
* wire/licorice rep aliases
* menu: A > copy to object
* new commands: copy_to, uniquify
* fix slow 'extract' performance
2017-08-02 Thomas Holder <thomas.holder@schrodinger.com>
* support "not ..." and "enabled" in name patterns.
(e.g.: delete not enabled)
* improve/fix unicode+utf-8 handling for labels
* iterate color settings: type int
(e.g.: iterate all, print(s.sphere_color))
* fix cmd.load with contents
https://sf.net/p/pymol/mailman/message/35966326/
* fix ray tracing of stick_ball + valence
https://sf.net/p/pymol/mailman/message/35928857/
* 1.8.7.0 (unstable/experimental)
2017-07-03 Thomas Holder <thomas.holder@schrodinger.com>
* web.pymolhttpd -> pymol.pymolhttpd
https://sf.net/p/pymol/bugs/148/
* make build reproducible
https://sf.net/p/pymol/patches/12/
2017-06-01 Thomas Holder <thomas.holder@schrodinger.com>
* new "label" selection operator
* alter_state: remove restriction on x/y/z/flags
* iterate/label: expose "state" for discrete atoms
* CTRL+L drag/click -> move/center in 3-Button-Viewing mode
* auto-detect $PREFIX/share/pymol as $PYMOL_PATH
* locale LC_NUMERIC=C float parsing/formatting
* Python 3: fix wrong PyCapsule_New destructor
2017-04-17 Thomas Holder <thomas.holder@schrodinger.com>
* Python 3: fix builder bond order buttons
(Red Hat Bug 1442127)
* fix MAE export PDB residue/atom names
* restored "scene_animation" setting (1.7.6 regression)
* restored "import cmd" prevention (1.8.6.0 regression)
* 1.8.6.1
2017-03-09 Thomas Holder, Piotr Rotkiewicz
* 1.8.6.0
2017-02-22 Thomas Holder <thomas.holder@schrodinger.com>
* fast MMTF load support in C++
* extra_fit: report RMS for method=cealign
Thanks to Hongbo Zhu
* CTRL-L ligand zoom
* preset > classified (auto_show_classified equivalent)
preset > interface (ported from Incentive PyMOL 1.8.0)
* set_key auto-completion
* command completion for selection language
* fix connect_mode=4 for N-H1 and N-H3
* fix CGO ALPHA and dup COLOR issue
* 1.8.5.1 (beta)
2017-01-19 Thomas Holder <thomas.holder@schrodinger.com>
* width/height arguments for movie export (mpng, movie.produce)
* fetch: support "fetch EMD-3489"
* auto_show_classified -1 => 3 for 500k+ atoms
* pick_shading => surface_color_smoothing off
* cleanup: eliminate pymol.pymol_launch variable
2016-12-14 Thomas Holder <thomas.holder@schrodinger.com>
* update molfile plugins to VMD version 1.9.3
* fetch 2fofc/fofc: update URLs, EDS will retire in 2017
* fix sf#102 pseudoatom multi-state problem
* editor.attach_amino_acid: fix PRO/N geometry
2016-12-05 Thomas Holder <thomas.holder@schrodinger.com>
* avoid selection keyword name conflicts, append underscore
* load: allow format=plugin (by extension) and format=plugin:PLUGIN
(with PLUGIN being a molfile plugin identifier)
* load format "vdb": VIPERdb PDB variant with retain_order=1
* load/load_traj: guess trajectory object
* fetch
* new setting "fetch_type_default"
* type=mmtf: fetch MMTF format
* type=2fofc/fofc: get spacegroup from PDBe API
* update download URLs
* new setting: editor_auto_measure
* new default: ray_transparency_oblique_power=4.0
* "update" command: support "current state" (-1)
* alter elem -> update protons and vdw
* don't allow "import cmd" (corrupts PyMOL namespace)
* support "python -m pymol" to launch PyMOL
* 1.8.5.0 (unstable/experimental)
2016-10-05 Thomas Holder <thomas.holder@schrodinger.com>
* 1.8.4.0
* setup.py: --no-launcher
2016-09-26 Thomas Holder <thomas.holder@schrodinger.com>
* pse_export_version: legacy scenes support
* use ignore_case setting with set_name command
* setup.py: detect anaconda prefix
* 1.8.3.3 (unstable/experimental)
2016-08-29 Thomas Holder <thomas.holder@schrodinger.com>
* experimental MMTF load support
* map export in CCP4 format
* SDF V3000 import/export support
* refactor molecular file formats export: Unified handling of PDB,
PQR, mmCIF, MOL2, SDF, XYZ, MAE
* PLY geometry import (as CGO)
* new command: unset_deep
* new setting: cartoon_all_alt: Create cartoon for every alt code
* stick_h_scale: default=1.0 (was: 0.4) but remove dependency on
negative stick_radius
* auto_show_classified: Visualize small (< 50 atoms) polymer
classified molecules like organic
* bymol selection operator: ignore zero-order bonds
* menu: isomesh/surface negative color
* improve alignment of residues with unknown resn (e.g. ligands):
give a match score of 5 to perfect matches of unknown residue codes.
Previously, those got match score -1.
* remove broken and obsolete "PMO" file support
* use "label_digits" setting with "label" command
* do not resize window when loading a session file
* fix ignored SCALE w/ identity rotation (e.g. 1WAP)
* fix "scene auto, clear" (Scene > Delete)
* new setting: pick_shading: do flat shading for programmable image
color analysis
* experimental cmd.raw_image_callback: post cmd.draw() callback
* 1.8.3.2 (unstable/experimental)
2016-05-26 Thomas Holder <thomas.holder@schrodinger.com>
* fix mutagenesis wizard "No Mutation" (update and rms commands)
* experimental FreeBSD support
* 1.8.2.1
2016-04-19 Thomas Holder <thomas.holder@schrodinger.com>
* 1.8.2.0
* get_sasa_relative (command ported from Incentive PyMOL)
* Color menu uses util.color_deep (ported from Incentive PyMOL)
* "C > by rep" (ported from Incentive PyMOL)
* fix crash when saving mesh PSE without map
2016-03-27 Jared Sampson
* new setting: collada_background_box (default 0)
https://sourceforge.net/p/pymol/mailman/message/34961984/
2016-03-21 Thomas Holder, Gabriel Marques
* pse_export_version: save 1.7.6 compatible PSEs by default
* forward "set" to "set_bond" for bond-level settings
* fetch: use http instead of ftp with default host
* MOL2 export
- chain support (write substructure record)
* MOL2 import
- more reliable resn reconstruction
- hetatm=0 for subst_type=RESIDUE
- don't use root atom id for substructure mapping
* set_name w/ map: update dependents (mesh, surface, volume)
* skip mmCIF "CA ATOMS ONLY" detection (not needed anymore)
* fix COLLADA export crash with transparency
* fix load_traj crash w/ state-level settings
* 1.8.1.2 (beta)
2016-03-03 Thomas Holder <thomas.holder@schrodinger.com>
* new setting: auto_show_classified
* cartoon/ribbon: auto-detect CA-only models
* mmCIF reading of full sequence now independent of cif_use_auth
* mmCIF ss assignment to full residue, not only CA
* fix selection macros with wildcards and colon (:) residue ranges
(1.8.0 regression)
* fix SCALE coordinate transformation for multi-model PDBs (e.g. 1hho)
* fix logging of expressions which contain '''
2016-02-08 Thomas Holder <thomas.holder@schrodinger.com>
* restore ignore_case=on default
* new setting: ignore_case_chain (default off)
https://sourceforge.net/p/pymol/mailman/message/34815599/
* new setting: cartoon_gap_cutoff
* increase PYMOL_MAX_THREADS
https://sourceforge.net/p/pymol/mailman/message/34787473/
* amber topology loading: bond order 1 for all bonds
https://sourceforge.net/p/pymol/mailman/message/34812536/
* improve MOL2 file handling
* new grid_mode=3: grid per object-state
2016-01-11 Thomas Holder <thomas.holder@schrodinger.com>
* distance mode=4: distance between centroids
* byring: new selection operator
* "Distances to Rings" mode in measurement wizard
* basic atom typing for MOL2 export
* cartoon dash: new dashed loop-like cartoon type
2015-12-14 Thomas Holder, Blaine Bell
* support segi, resn and name of arbitrary string length
* expose settings to iterate/alter via "s.<name>" (available
in Incentive PyMOL since 1.7.0)
* Python 3 compatibility for champ module
https://sf.net/p/pymol/bugs/172/
* apbs_tools: apply fixes from Pymol-script-repo
2015-12-09 Thomas Holder <thomas.holder@schrodinger.com>
* Python 3 compatibility, tested with Python 2.6, 2.7 and 3.4
* 1.8.1.0 (unstable/experimental)
2015-11-18 Thomas Holder, Blaine Bell, Gabriel Marques
* 1.8.0.0
* Tcl/Tk Settings GUI: feedback, radio buttons, font size dialog
* default alignment_as_cylinders changed to off
2015-10-15 Thomas Holder <thomas.holder@schrodinger.com>
* new default: scene_buttons=on
* normalize_ccp4_maps=2 -> use mean and stdev from file header
* fix alignment with atoms w/o coords in a state
2015-10-06 Thomas Holder <thomas.holder@schrodinger.com>
* new filetypes: pdbml, pdbqt, cml
* cell/symmetry: accept alpha=beta=gamma=0.0 as 90.0
* leave unknown protons as -1 instead of 0 (lonepair), fixes
vdw assingment for unknown elements (1.8 instead of 0.5)
* reimplement reading full sequence from mmCIF. Only with
cif_use_auth=off and retain_order=off. Fill in missing
CA atoms for polypeptides.
* new API function cmd.get_object_ttt()
* APBS Plugin: --whitespace argument for pdb2pqr
* fix scene next/previous, was broken on Windows 10
* fix split_states with non-unique titles
* fix "File > Run" fails if path has spaces
2015-08-30 Thomas Holder <thomas.holder@schrodinger.com>
* fix cartoon_trace_atoms for beta-sheets
* fast connect_mode=4: Add $PYMOL_DATA/chem_comp_bond-top100.cif
which is a subset of the components.cif dictionary and contains
only bond records for the 100 most frequent monomers in the PDB.
Download other monomers on-demand from PDBeChem.
2015-08-12 Thomas Holder <thomas.holder@schrodinger.com>
* cif_keepinmemory, pymol.querying.cif_get_array (experimental)
* ramp_update (new command)
* ramp objects now have "A > Range > ..." and "C > ..." menus
* mmCIF _chem_comp_atom:
- skip atoms with missing coordinates
- prefer ideal over model coordinates
* cmd.set_key() decorator support
2015-07-29 Thomas Holder <thomas.holder@schrodinger.com>
* fix isosurface all_states rendering
* pdb_hetatm_guess_valences for CIF loading
* mutagenesis wizard: improve "apply" performance
* fix measurement and alignment object partial PSE loading
* some load/save refactoring
* keep atom IDs when creating object from selection
* when renaming group "A" to "B", then also rename entry "A.X" to "B.X"
2015-07-02 Thomas Holder <thomas.holder@schrodinger.com>
* mmcif: match pdb1, pdb2, ... files with assembly generation
- fix handling of _pdbx_struct_assembly_gen with repeated asym_id
- create assembly for multi-state objects
- no pdb_insure_orthogonal for assemblies
* fix "File > Run"
2015-06-23 Thomas Holder <thomas.holder@schrodinger.com>
* fix assemblies for cases like 4f3r which have multiple entries in
the _pdbx_struct_assembly_gen table
* fix ref counts in iterate/alter subscripts
* improve side_chain_helper and nucleic_adic_mode situation
* eliminate all "try/catch" blocks for std::map lookups
* clean up some MemoryDebug stuff and remove unused jenarix wrapper
2015-06-17 Thomas Holder <thomas.holder@schrodinger.com>
* Experimental: cmd.get_assembly_ids
* mmCIF: support "_atom_site.pdbe_label_seq_id"
* mmCIF: set "ignore" flag for HETATMSs (no surface)
* improve memory usage and performance of components.cif parsing
2015-06-10 Thomas Holder <thomas.holder@schrodinger.com>
* fetch 'cif' by default (was: pdb)
* warn if selecting with lower-case arguments to help identifying
legacy selections which are incompatible with ignore_case=0
* port selection macro parsing from Python to C
* fix https://sf.net/p/pymol/bugs/169/ (cmd.fab() with existing object
name produces unexpected results and downstream segfault)
2015-05-20 Thomas Holder <thomas.holder@schrodinger.com>
* change default (!) of "ignore_case" setting to off. Case insensitve
identifier matching is not practical anymore with large structures
which use upper and lower case chain identifiers.
* new setting "assembly" to load assemblies from mmCIF as multi-state
objects with all_states=1
* new setting "cif_use_auth" controls whether mmCIF "auth" identifiers
are used or not (on by default)
* mmCIF "CA/P ATOMS ONLY" chains: set atom-level cartoon_trace_atoms
and ribbon_trace_atoms
* CIF discrete and irregular multi-model loading support
* support "pdb_honor_model_number" setting for CIF
* load multiple objects ("data_" blocks) from one CIF file (multiplex=-1)
* don't store AtmToIdx, DiscreteAtmToIdx or DiscreteCSet to PSE
(unless pse_export_version <= 1.76)
* 1.7.7.1 (unstable/experimental)
2015-05-04 Thomas Holder, Blaine Bell, Gabriel Marques
* 1.7.6.0
* VASP file support for: CHGCAR, OUTCAR, POSCAR, XDATCAR
* psf file support
* ignore SCALE matrices with negative determinant
* fix crash when loading malformed CIF file
* fix cif export for natoms = 0
* fix several memory leaks
* fix crash when saving PSE with deleted ramp
2015-04-20 Thomas Holder <thomas.holder@schrodinger.com>
* new setting: pse_export_version to save to old session formats
* fix memory leak in get_global_components_bond_dict
* change setting default: pdb_conect_nodup 0 -> 1
* fix Tcl/Tk File menu unicode handling
* fix auto-complete for filenames with spaces
* mmCIF: support CHEM_COMP_BOND from mmCIF file
* residue information for MOL2 export
2015-03-12 Thomas Holder, Blaine Bell, Gabriel Marques
* mmCIF _atom_sites.fract_transf support (SCALEn equivalent)
* Complete port of scenes to C++
* warn user if setting a setting on the wrong level
* cmd.extendaa: shortcut for cmd.extend with argument auto-completion
* reduced memory footprint of AtomInfoType
* expose "reps" to iterate/alter
* expose "protons" to iterate/alter
* adaptive cartoon quality and sampling, depending on number of atoms
* fix ring center color with cartoon_ring_color=default
* make SelectorGetTmp strictly molecular, fixes for example "dss" with
group names
* fix "copy" can cause crash
* fix "custom" selection operator
* consider spec_count in shaders
* don't invalidate shaders for lighting settings
* don't disable shaders for all Intel chips
* don't touch sphere_mode when disabling shaders
* map_new buffer == -1 -> gaussian_resolution
* fix all_states picking
* remove cylinder_shader_ff_workaround and cylinders_shader_filter_faces
* remove unused gl_ambient setting
* fix Tcl/Tk menu settings logging
* fix: grid mode scales down label size incorrectly
* fix: no animate argument for cmd.origin
* fix side_chain_helper for hetatm polymer atoms
* fix .mmd export
* refactor many function to take "const" pointer arguments
* 1.7.5.0 (unstable/experimental)
2014-12-03 Thomas Holder, Blaine Bell, Gabriel Marques
* 1.7.4.0
2014-12-02 Thomas Holder <thomas.holder@schrodinger.com>
* use COMPONENTS_CIF environment variable to look for components.cif
* update fetchHosts and hostPaths URLs
* 1.7.3.6 (unstable/experimental)
2014-11-20 Thomas Holder <thomas.holder@schrodinger.com>
* cif: read first_model_num
* fixed _foo?bar lookup could fail in mmCIF parsing
* deprecated full_screen setting (use full_screen command)
* 1.7.3.4 (unstable/experimental)
2014-10-19 Jared Sampson, Thomas Holder
* COLLADA (dae) export support.
Implemented by Jared Sampson as his POSF project.
* 1.7.3.2 (unstable/experimental)
2014-10-16 Thomas Holder, Blaine Bell
* fast PDBx/mmCIF and core CIF loading in C++
* new connect_mode=4 does bonding with components.cif dictionary
(mmCIF only, components.cif needs to be present in current
directory)
* gray out residues in the sequence viewer that are missing from the
current state; Read missing residues from mmCIF files
(_pdbx_unobs_or_zero_occ_residues records) so that they show up in
the sequence viewer
* add spider map reading support
* load "map" as ccp4 instead of throwing "ambiguous" error
* xyz write support
* Improve right-button zoom: use origin instead of clipping slab
center as depth indicator, fixes zoom speed when far clipping plane
is very far away
* don't use dynamic_width for nonbonded rep
* 1.7.3.1 (unstable/experimental)
2014-09-17 Thomas Holder, Blaine Bell
* ignore SCALEn if CRYST1 is 1x1x1 or invalid
* new/refactored API functions for accessing coordinates and maps
as numpy arrays:
* load_coords
* load_coordset (was: load_coords)
* get_coords
* get_coordset
* get_volume_field now returns numpy array
* new API function: cmd.set_state_order
* Session file (PSE) support for callback objects
* fix/silence many compiler warnings
* fix bg_rgb_top/bg_rgb_bottom side effects
* revert "fix setting surface_circumscribe"
* delete some obsolete files
2014-09-08 Thomas Holder <thomas.holder@schrodinger.com>
* migrate all C files to C++ (rename c -> cpp)
* multi-letter chain support
* added missing function pymol.menu.measurement_color
* fix small regression bug in pymol.creating.unquote
2014-09-04 Thomas Holder, Blaine Bell
* 1.7.3.0 (unstable/experimental)
* sync various pieces of code with Incentive PyMOL
* faster iterate/alter implementation ported from Incentive PyMOL
* experimental mmCIF write support (atoms only)
* partial multi-letter chain support
* super: use guide instead of CA, enables nuc acid alignment
* fix movie panel not shown until resize
* eliminate some deprecated parsing modes
* python: convert some files to absolute_import
* --help and --version
* dynamic_measures refactoring, fixes duplicated IDs bug
* get_type returns object:alignment and object:ramp
* new "command" Wizard ported from Incentive PyMOL
2014-08-15 Thomas Holder, Blaine Bell
* reimplement volume carving
- use a carve mask texture
* fix boxed volume around selection (with or without carving)
- this only worked for symmetry expanded volumes
- still limited to maps with symmetry information (TODO)
* removed ObjectVolumeGetIsUpdated, deprecate get_volume_is_updated
* refactored ObjectVolumeStateGetField, ObjectVolumeGetField
- don't keep a redundant vs->volume copy in memory
* revert a 1.7.2 opaque_background change
- real-time rendering background was always black with
opaque_background=0
- removes opaque_background support for "draw"