is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source version.
| ChangeLog (pymol-v1.8.6.0.tar.bz2) | : | ChangeLog (pymol-v2.1.0.tar.bz2) |
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| ========================================================================= | | ========================================================================= |
| CHANGE LOG | | CHANGE LOG |
| ========================================================================= | | ========================================================================= |
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|
| | 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 | | 2017-03-09 Thomas Holder, Piotr Rotkiewicz |
| | |
| * 1.8.6.0 | | * 1.8.6.0 |
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| 2017-02-22 Thomas Holder <thomas.holder@schrodinger.com> | | 2017-02-22 Thomas Holder <thomas.holder@schrodinger.com> |
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| * fast MMTF load support in C++ | | * fast MMTF load support in C++ |
| | |
| * extra_fit: report RMS for method=cealign | | * extra_fit: report RMS for method=cealign |
| Thanks to Hongbo Zhu | | Thanks to Hongbo Zhu |
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| End of changes. 1 change blocks. |
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| 0 lines changed or deleted | | 170 lines changed or added |
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