分子3D绘图【知识荟萃】

1、分子3D绘图,1,行业重点,一、计算化学背景,1.1 计算机的发展硬件背景,大量原来无法想象的计算可以轻易完成,计算机的硬件和其他技术高速发展,计算速度高速增长,CPU能力 多核技术,GPU技术 并行技术,Tesla K80 8.74TFlops v.s. Blue Gene/L 135.58.74TFlops,Knights Landing Xeon Phi 3TFlops,E7-8890V4 24核,2,行业重点,Performance Development,3,行业重点,K computer 2011.62012.5,Tianhe-1A 2010.102011.5,Sequoia -

2、BlueGene/Q 2012.6-2012.10,Titan 2012.112013.5,Tianhe-2 2013.62016.6,曾 经 的 Top 1,Sunway TaihuLight 2016.6,4,行业重点,48th TOP10 November 2016,中国有171台超级计算机入围TOP 500,5,行业重点,软件的发展使用户勿需具备高深的理论知识，只要有一般的计算机应用能力，就可以很容易地完成许多计算化学的简单工作。,1.2 计算化学软件的发展,1.3 计算化学的应用,The prediction of the molecular structure of molecul

3、es by the use of the simulation of forces, or more accurate quantum chemical methods, to find stationary points on the energy surface as the position of the nuclei is varied. Storing and searching for data on chemical entities (see chemical databases). Identifying correlations between chemical struc

4、tures and properties (QSPR/ QSAR). Computational approaches to help in the efficient synthesis of compounds. Computational approaches to design molecules that interact in specific ways with other molecules (e.g. drug design and catalysis).,6,行业重点,1.4 常用分子模拟软件,Gaussian 98 GaussView 2.x Gaussian 03 Ga

5、ussView 3.x, 4.x Gaussian 09 Gauss View 5.x ,7,行业重点,HyperChem Professional 8.010 ChemBioOffice Ultra 14.0 Suit GAMESS ver. Aug 8, 2016 Free /GAMESS/ PC GAMESS/Firefly version 8.2.0 http:/classic.chem.msu.su/gran/gamess/index.html NWChem 6.6 Free ,

6、Materials Studio 图形计算平台，密度泛函，分子，溶剂，材料 Insight II 图形计算平台，生物分子 Schrdinger Suite 图形计算平台 SYBYL 图形计算平台,8,行业重点,GROMACS 5.1.4 Free /,TINKER 7.1 Free /tinker/,AMBER 16 /,NAMD 2.12 Free /Research/namd/,9,行业重点,ADF密度泛函，分子，溶剂，周期体系，

7、相对论，图形用户界面 AIM2000 分子中的原子，图形用户界面 AMPAC 半经验方法，图形用户界面 ArgusLab 从头计算，半经验方法，分子力学，图形用户界面 CHARMM 分子力学，蒙特卡罗 CRYSTAL 从头计算，密度泛函，周期体系 DMol 密度泛函，分子，周期体系 Jaguar 从头计算，密度泛函，分子，溶剂 MOLPRO 从头计算，密度泛函 PCMODEL 半经验方法，分子力学，图形用户界面 PyMol 分子模型显示 Q-Chem 从头计算，密度泛函，分子，溶剂 Spartan 从头计算，密度泛函，半经验方法， 蒙特卡罗，分子力学，图形用户界面，分子，溶剂 VASP (VA

8、MP) 密度泛函，分子动力学，赝势，平面波，材料 Discovery Studio QSAR，图形用户界面,10,行业重点,数据类型(最常见、纯文本格式) ENT/PDBBrookhaven Protein Data Bank MOL Molecular Design, Ltd. MDL HIN Hyperchem GJF Gaussian MOL2 Tripos CIF Crystallographic Information file,二、分子3D结构数据,11,行业重点,HETATM 1 C UNK 1 1.209 0.698 0.000 HETATM 2 C UNK 1 1.209 -

9、0.698 0.000 HETATM 3 C UNK 1 0.000 -1.397 0.000 HETATM 4 C UNK 1 -1.209 -0.698 0.000 HETATM 5 C UNK 1 -1.209 0.698 0.000 HETATM 6 C UNK 1 0.000 1.397 0.000 HETATM 7 H UNK 1 0.000 2.484 0.000 HETATM 8 H UNK 1 2.151 1.242 0.000 HETATM 9 H UNK 1 2.151 -1.242 0.000 HETATM 10 H UNK 1 0.000 -2.484 0.000 H

10、ETATM 11 H UNK 1 -2.151 -1.242 0.000 HETATM 12 H UNK 1 -2.151 1.242 0.000 CONECT 1 6 2 8 CONECT 2 1 3 9 CONECT 3 2 4 10 CONECT 4 3 5 11 CONECT 5 4 12 6 CONECT 6 1 7 5 CONECT 7 6 CONECT 8 1 CONECT 9 2 CONECT 10 3 CONECT 11 4 CONECT 12 5 END,BEN.ENT Brookhaven PDB,12,行业重点,BEN.GJF Gaussian,%chk=H:ben.c

11、hk # B3LYP/6-31G* opt Ben 0 1 C C 1 B1 C 2 B1 1 A C 3 B1 2 A 1 D1 C 4 B1 3 A 2 D1 C 1 B1 2 A 3 D1 H 1 B2 6 A 5 D2 H 2 B2 1 A 6 D2 H 3 B2 2 A 1 D2 H 4 B2 3 A 2 D2 H 5 B2 4 A 3 D2 H 6 B2 1 A 2 D2 B1 1.40 B2 1.08 A 120. D1 0. D2 180.,13,行业重点,BEN.GJF Gaussian,%chk=H:ben2.chk #b3lyp/6-31g(d) opt=vtight B

12、en 0 1 C 0.00000000 0.00000000 0.00000000 C 0.00000000 0.00000000 1.39661073 C 1.20949937 0.00000000 2.09491637 C 2.41900048 0.00000000 1.39661228 C 2.41900048 0.00000000 0.00000155 C 1.20950111 0.00000000 -0.69830409 H -0.94138405 0.00000000 -0.54350900 H -0.94138538 0.00000000 1.94011906 H 1.20949

13、890 0.00000000 3.18193419 H 3.36038453 0.00000000 1.94012127 H 3.36038586 0.00000000 -0.54350678 H 1.20950158 0.00000000 -1.78532191,14,行业重点,C -0.25 -0.47 0.00 O -0.25 0.96 0.00 H 0.77 -0.83 0.00 H -0.77 -0.83 0.89 H -0.77 -0.83 -0.89 H -1.16 1.28 0.00,内坐标输入(Z-Matrix),C C 1 1.54 H 1 1.09 2 109.47 H

14、1 1.09 2 109.47 3 -120. H 1 1.09 2 109.47 3 120. H 2 1.09 1 109.47 3 180. H 2 1.09 1 109.47 6 -120. H 2 1.09 1 109.47 6 120.,笛卡儿坐标输入,15,行业重点,结构数据的获得,简单分子可通过标准键长、键角、二面角数据直接写出 简单分子也可通过分子图形软件构建 有单晶结构数据的复杂分子，可直接转化 采用分子图形软件构建复杂分子，由于其构象存在多种可能性，因此必须通过适当的构象搜索方法方可得到合理的结构 对于大分子(如蛋白质)，其结构构建本身就是专门的计算化学研究的课题，只有通

15、过特定的方法(如同源模建等)方可得到可能的合理结构,16,行业重点,The Cambridge Crystallographic Data Centre (CCDC) http:/www.ccdc.cam.ac.uk/ Crystallography Open Database RCSB Protein Data Bank / The Worldwide Protein Data Bank /,晶体数据,17,行业重点,三、绘图软件简介,直接使用各种分子模拟显示软件 Chem3D, GaussView, Viewerli

16、te, Chimera, HyperChem, Argulab, Gabedit, Molekel RASMOL, VMD，MOLDEN, POVRAY 先用分子模拟软件输出POV文件，再用POVRAY渲染,18,行业重点,ViewerLite 5.0,安装文件小 5.7M 高水准分子显示功能 对晶体、蛋白质核酸有特殊显示功能 支持输入文件格式多 可直接输出较高水平的图片 支持输出专业3D渲染软件POVRAY 支持链接文件类型直接打开 其它版本 ViewerPro 4.2, 6.0 新版本 Discovery Studio 2016 Client,19,行业重点,.msv (Viewer bi

17、nary file format .pdb .ent (Brookhaven Protein Data Bank) .mol .sdf .sd .mdl (Molecular Design, Ltd. MDL) .car (Accelrys, Insight II) .csd .fdat .dat (Cambridge Structural Database Crystallographic files) .mol2 (Tripos) .msf (Accelrys, QUANTA),.msi (Accelrys, Cerius2) .cpd (Accelrys, Catalyst) .chm

18、(Accelrys, Catalyst Query) .cif (Crystallographic Information File) .xyz (generic) .skc (MDL, ISIS) .grd (Accelrys, Insight II Grid File) .wvc (Viewer Command File),ViewLite支持输入文件格式,20,行业重点,21,行业重点,ViewerPro介绍,ViewerPro有4.2和6.0等版本，其与ViewLite一般的功能差别不是特别大，主要增加了编辑工具(一般不用)以及多光源显示效果等。,22,行业重点,Discovery S

19、tudio Client,23,行业重点,HyperChem,商业软件 集成了分子构建、分子力学、 量子力学、分子动力学等 分子构建功能极好 完备的说明书,24,行业重点,GaussView,商业软件 配合Gaussian使用,25,行业重点,Chem3D,商业软件 使用广泛,26,行业重点,ArgusLab A molecular modeling, graphics, and drug design program,27,行业重点,UCSF Chimera,UCSF Chimera is a highly extensible program for interactive visuali

20、zation and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.,/chimera/,28,行业重点,Molekel is a

21、n open-source multi-platform molecular visualization program.,http:/ugovaretto.github.io/molekel/,29,行业重点,VMD /Research/vmd/ Support for all major computer platforms Support for multicore processors Support for GPU accelerated computation Gabedit Molden http:/www.cmbi.ru.nl/mold

22、en/ a variety of graphics instructions; postscript, XWindows, VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and Figure RASMOL /,30,行业重点,POVRAY绘制高水平3D图,POV-Ray，全名是Persistence of Vision Raytracer，是一个使用光线跟踪绘制三维图像的开放源代码免费软件。运行POV脚本语言。,/,31,行业重点,32,行业重点,33,行

23、业重点,4.1 构建椅式环己烷(球棍),选择Draw工具,拖动鼠标画出六边形 BuildAdd H #declare _WLVP_dot_size = 0.03; #declare _WLVP_text_depth = 0.0; #declare _WLVP_text_scale = 0.3; #declare _WLVP_finish = finish diffuse 0.9 ambient 0 specular 0.4 roughness 0.2 ,相机,灯光,背景,定义变量,ViewerLite打开分子结构数据 调整显示角度至满意 FileSave as POV格式,46,行业重点,un

24、ion sphere , 0.290625 translate pigment rgbt finish _WLVP_finish sphere , 0.206250 translate pigment rgbt finish _WLVP_finish . cylinder , , 0.090000 pigment rgbt finish _WLVP_finish cylinder , , 0.090000 pigment rgbt finish _WLVP_finish matrix translate scale 0.8 ,球,棍,整体旋转,整体平移,半径,位置,颜色,半径,棍两端坐标,材质

25、,47,行业重点,finish diffuse 0.9 ambient 0 specular 0.4 roughness 0.2 ,finish diffuse 0.9 ambient 0 specular 0.74 roughness 0.002 ,48,行业重点,camera orthographic location right -4/4*x angle 90.0 look_at light_source rgb parallel point_at light_source rgb parallel point_at shadowless light_source rgb paralle

26、l point_at light_source rgb parallel point_at background color rgb #declare Scale=5; #declare C3L = 16/Scale; #declare C2L = 16/Scale; #declare F = finish specular 0.4 roughness 0.005 diffuse 0.8 ambient 0.2 #declare FGlass = finish specular 0.6 roughness 0.002 ambient 0.2 diffuse 0.8 reflection 0.2

27、, 0.5 conserve_energy #declare FMetal = finish ambient 0.4 brilliance 2 diffuse 0.8 metallic specular 0.90 roughness 0.002 reflection 0.1 #declare C3T= object prism linear_sweep linear_spline -0.025, / sweep the following shape from here . 0.025, / . up through here 4, / the number of points making

28、up the shape . , , , pigment rgbt rotate rotate finishFMetal /triangle #declare C3= union cylinder, 0.25/Scale pigment rgbt finishFMetal objectC3T scale 7/Scale translate objectC3T scale 7/Scale translate rotate #declare C2 = union cylinder, 0.25/Scale pigment rgbt finish FMetal cylinder,0.2 scale x

29、*2 rotate rotate scale 2/Scale translate pigmentrgbt finish FMetal cylinder,0.2 scale x*2 rotate rotate scale 2/Scale translate pigmentrgbt finish FMetal ,49,行业重点,# declare MOL= union sphere , 0.348750 translate pigment rgbt finish F sphere , 0.348750 translate pigment rgbt finish F sphere , 0.34875

30、0 translate pigment rgbt finish F sphere , 0.348750 translate pigment rgbt finish F sphere , 0.348750 translate pigment rgbt finish F sphere , 0.348750 translate pigment rgbt finish F sphere , 0.247500 translate pigment rgbt finish F sphere , 0.247500 translate pigment rgbt finish F sphere , 0.24750

31、0 translate pigment rgbt finish F sphere , 0.247500 translate pigment rgbt finish F sphere , 0.247500 translate pigment rgbt finish F sphere , 0.247500 translate pigment rgbt finish F sphere , 0.247500 translate pigment rgbt finish F sphere , 0.247500 translate pigment rgbt finish F sphere , 0.24750

32、0 translate pigment rgbt finish F sphere , 0.247500 translate pigment rgbt finish F sphere , 0.247500 translate pigment rgbt finish F sphere , 0.247500 translate pigment rgbt finish F cylinder , , 0.06 pigment rgbt finish F cylinder , , 0.06 pigment rgbt finish F cylinder , , 0.06 pigment rgbt finis

33、h F cylinder , , 0.06 pigment rgbt finish F cylinder , , 0.06 pigment rgbt finish F cylinder , , 0.06 pigment rgbt finish F cylinder , , 0.06 pigment rgbt finish F cylinder , , 0.06 pigment rgbt finish F cylinder , , 0.06 pigment rgbt finish F cylinder , , 0.06 pigment rgbt finish F cylinder , , 0.06 pigment rgbt finish F cylinder , , 0.06 pigment rgbt finish F cylinder , , 0.06 pigment rgbt finish F cylinder , , 0.06 pigment rgbt finish F cylinder , , 0.06 pigment rgbt finish F cylinder , , 0.06 p