- 計算殘基的暴露程度
- 直接下載biological unit
以下的資訊翻譯自«PyMOL v1.8.0.0 Notes»，有些不知道要怎樣翻的，或是覺得無趣的就保留原文。
新的功能
- (mm)CIF：這是一種新的PDB format，可以處理很大的巨分子
- add support for discrete=1 loading of CIF files
- 改善multi-model分子下載
- 支援下載多個物件
- 支援_symmetry_equiv.pos_as_xyz, _space_group_symop.operation_xyz
- set cartoon_trace_atoms and ribbon_trace_atoms for CA-only models
- 直接下載biological unit，但這要把assembly設定打開
- Ignore “auth” identifiers with cif_use_auth=off (default: on)
- 修改讀取mmCIF完整序列的方式
- Improve connect_mode=4 support and performance: Bonding for most common residue types provided in $PYMOL_DATA/chem_comp_bond-top100.cif. Other types are downloaded on the fly from PDBeChem.
- read metalc and disulf bonds
- 新的檔案格式
- PDBQT
- Basic support for PDBML (.xml and .xml.gz extensions)
- Basic support for CML
- fetch：抓取檔案的時候用type=cc，可以從PDBeChem (3-letter codes)下載
- Render：用虛線畫zero-order bonds
- 計算殘基的暴露程度(relatiev solvent accessible surface area per residue)，計算方式是用指令 get_sasa_relative，或是從選單上 A > compute > surface area > per residue
Refactoring
這段都是在說改善了程式的效能
PyMOL API
- cmd.set_keys()
- cmd.get_object_ttt()
設定
- 改變預設 ignore_case=off
- 新設定 assembly
- 新設定cif_use_auth
- 新設定 cif_keepinmemory 實驗性質
- 新設定 pse_binary_dump 實驗性質，讓PSE輸出可以更快且更有效率地用記憶體
- 改變預設 scene_buttons=on 未來存Scene會直接有按鈕出現
- 改變預設 alignment_as_cylinders=off
其他Misc
- Symmetry/Cell loading: accept alpha=beta=gamma=0.0, assume orthogonal cell (alpha=beta=gamma=90.0)
- Set protons for unknown atoms to -1 instead of 0 (0 is interpreted as lonepair)
- Properties:
- alter: derive property type from python type
- alter: list(p) → list of property names
- Real-time ray_transparency_oblique with shaders
- Keep IDs when creating new object from selection (restore pre-1.4 behavior)
- Updated bundled Schrödinger library for atom typing and stereochemistry (text_type and stereo labeling)
- Tcl/Tk Menus:
- Radiobuttons for all setting switches
- Feedback to console when changing a setting
- Simple font size dialog (Setting > GUI Font Size)
Mobile PyMOL
Chromadepth: The Stereo 3D button is now a 3-state toggle button (Off / Anaglyph / Chromadepth)
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