分子3D绘图

单击此处编辑母版标题样式,单击此处编辑母版文本样式,第二级,第三级,第四级,第五级,#,Nankai University,“魅力计算演绎分子”,南开大学化学学院计算化学知识技能大赛,2017.3.21,分子,3D,绘图,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,Performance Development,K computer,2011.62012.5,Tianhe-1A,2010.102011.5,Sequoia - BlueGene/Q,2012.6-2012.10,Titan,2012.112013.5,Tianhe-2,2013.62016.6,曾 经 的,Top 1,Sunway TaihuLight,2016.6,Rank,Name,Man.,Country,Total Cores,Rmax,(TFlop/s),Power,1,Sunway,NRCPC,China,10649600,93014.6,15371,2,Tianhe-2,NUDT,China,3120000,33862.7,17808,3,Titan,Cray Inc.,United States,560640,17590.0,8209,4,Sequoia,IBM,United States,1572864,17173.2,7890,5,Cori,Cray Inc.,United States,622336,14014.7,3939,6,Oakforest-PACS,Fujitsu,Japan,556104,13554.6,2719,7,K Computer,Fujitsu,Japan,705024,10510.0,12660,8,Piz Daint,Cray Inc.,Switzerland,206720,9779.0,1312,9,Mira,IBM,United States,786432,8586.6,3945,10,Trinity,Cray Inc.,United States,301056,8100.9,4232,48,th,TOP10,November 2016,中国有,171,台超级计算机,入围,TOP 500,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 molecules 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 structures 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,).,1.4,常用分子模拟软件,Gaussian 98 GaussView 2.x,Gaussian 03 GaussView 3.x, 4.x,Gaussian 09,Gauss View 5.x,http,:/ Professional 8.010,http,:/ Ultra 14.0 Suit,GAMESS ver. Aug 8, 2016,Free,http,:/www.msg.chem.iastate.edu/GAMESS/,PC GAMESS/Firefly version,8.2.0,http,:/classic.chem.msu.su/gran/gamess/index.html,NWChem 6.6,Free,http,:/www.nwchem-sw.org,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,GROMACS,5.1.4,Free,http:/www.gromacs.org/,TINKER,7.1,Free,http:/dasher.wustl.edu/tinker/,AMBER,16,http:/ambermd.org/,NAMD,2.12,Free,http:/www.ks.uiuc.edu/Research/namd/,ADF,密度泛函，分子，溶剂，周期体系，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,(VAMP),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,数据类型,(,最常见、纯文本格式,),ENT/PDB,Brookhaven 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,HETATM 1 C UNK 1 1.209 0.698 0.000,HETATM 2 C UNK 1 1.209 -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,HETATM 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,BEN.GJF Gaussian,%chk=H:ben.chk,# 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.,BEN.GJF Gaussian,%chk=H:ben2.chk,#b3lyp/6-31g(d,),opt=vtight,Ben,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,1.20949890 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,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 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,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，只有通过特定的方法,(,如同源模建等,),方可得到可能的合理结构,The Cambridge Crystallographic Data Centre (CCDC),http:/www.ccdc.cam.ac.uk/,Crystallography Open,Database,http,:/ Protein Data Bank,http:/www.rcsb.org/,The Worldwide Protein Data Bank,http:/www.wwpdb.org/,晶体数据,三、,绘图软件简介,直接使用各种分子模拟显示软件,Chem3D, GaussView, Viewerlite, 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,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,.msv (Viewer binary 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 (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,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。,Discovery,Studio Client, molecular modeling, graphics, and drug design program, Chimera,UCSF Chimera is a highly extensible program for interactive visualization 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.,http:/www.cgl.ucsf.edu/chimera/,Molekel is an open-source multi-platform molecular visualization program.,http:/ugovaretto.github.io/molekel/,VMD,http:/www.ks.uiuc.edu/Research/vmd/,Support for all major computer platforms,Support for multicore processors,Support for GPU accelerated computation,Gabedit, variety of graphics instructions;,postscript, XWindows, VRML, povray, OpenGL, tekronix4014, hpgl, hp2392 and Figure,RASMOL,http:/www.openrasmol.org/,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。,http:/www.povray.org/,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,Build,Add H & Model Build,将构建的分子按标准键长键角构造，本例为椅,式环己烷,选择,Rotate out-of-plane,调整到适宜角度,可用分子力学优化,DisplayRendering,选择分子显示模式，如,Ball and Cylinders,球棍模型可调整球的大小和棍的粗细。,可保存结构数据或拷贝图形,四、分子构建,-HyperChem,4.2,构建苯、环戊二烯、茂环,选择,Draw,工具,拖动鼠标画出六边形,在六边形内靠近键处双击,Build,Add,H & Model Build,将,构建成苯,选择,Draw,工具,拖动鼠标画,出五边形,在五边形相隔两键单击,Build,Add H & Model,Build,构建成,环戊二烯,选择,Draw,工具,拖动鼠标画出五边形,在,五边形内,靠近键处,双击,Build,Add H & Model Build,构建成,环戊二烯自由基（茂环）注意与环戊二烯差别,环戊二烯自由基，,Draw,工具,鼠标右键去掉共轭,画双键，,Build,Add H & Model Build,构建成,环戊二烯,4.3,构建联苯,Draw,工具,拖动画出联苯,Select,工具,(Select,菜单中选项为,Atom),在联苯两苯环间的键上双击,Rotate out-of-plane,工具转动分子,Rotate in-plane,工具鼠标右键旋转选定的苯环,也可以选择代表苯环夹角的,4,个原子,(,二面角,),，,Edit-Set Bond Torsion,通过设定二面角来调整两苯环夹角,4.4,构建二茂铁,Draw,工具,拖动画出五元环,在,五元环,内,靠近键处双击,Build,Add H & Model Build,构建成环戊二烯自由基（茂环,）,Select-,选,Molecule,选项,Select,工具,茂,环上单,击选中,茂,环,复制，粘贴产生第二个茂环,鼠标右键在空白处单击，撤消选择,鼠标单击一个茂环,鼠标单击,translate,工具,按鼠标右键拖动到两个,茂,环重合,选,Rotate out-of-plane,按鼠标左键转动两茂环到垂直位置,鼠标单击,translate,工具，,按鼠标右键拖动到两个茂,环拉开一定距离,双击,，周期表中选,Fe,在茂环间加上,Fe,旋转整个分子，调整,Fe,在中心，也可将上下茂环调成交叉式。,4.5,构建五角十二面体烷,Draw,工具,画出五角十二面体,烷的连接图,Build,Add,H & Model Build,构建,按空格键可自动调整分子大小,按,Magnify/Shink,工具，拖动可放大,/,缩小分子,4.6,构建,C,60,Draw,工具,画,出图示部分,Build,Add,H & Model Build,构建,删除上面所有的氢，复制为,2,个,按二茂铁方式将两个锅形交叉合在一起,连接相邻的,C,并设共轭,Build,Add H & Model Build,构建,构建后可用半经验,PM3,优化,如感觉不好操作，也可逐层加最后合为,C,60,4.7,构建,船式,环己烷、环辛四烯,构建椅式环己烷,用,选择工具,选择相对的两个,C-C,键,Select-Name Selction-Plane,定义平面,选择右半部分,Edit-Reflect,按定义平面翻转所选部分，构成船式环己烷,构建环辛四烯（构建出椅式，错误）,仿照,船式,环己烷构建方法构建成正确的结构,4.7,构建,1, 3,交替式杯,4,吡咯,直接由右图构建杯,4,吡咯不易保证构象，可在中间加一个,C,Build,Add H & Model Build,构建,工具右击删除,C,选择,4,个,N,Build,Add Hydrogens,得到,1, 3,交替式杯,4,吡咯,可进一步优化,HyperChem,构建的环己烷,另存为,mol,格式,(,或,mol2),文件,Viewerlite,打开相应文件,单击,显示样式按钮，选择分子模型的样式,左工具栏调整模型角度、大小和位置,View-O,ptions,调整显示参数、光源等,可保存为位图,(,可设置图片大小,),五、,ViewerLite,绘图,5.1,绘制椅式环己烷,ViewOption,可调整背景颜色,可设置,depth cue,用雾状效果分清原子前后位置,可设置透视效果,Tools,Hydrogen,可隐藏,/,显示 增加,/,移除,H,原子,Monitor,可标记原子间距离、键角、二面角，氢键等,Surface,可绘制分子表面,pdb,格式的晶体数据文件可从网上获得，也可自己编辑,打开,ZnS(c).pdb,Display Style,设置原子显示模式，,Cell,选择,line (,红色,),调整角度，设置效果光源等,可,保存,为,.msv,格式,，也可输出图片,Tools-Crystal Cell,可,显示多晶胞,5.2,绘制,立方,ZnS,晶体,5.3,绘制,蛋白质和核酸,pdb,格式的晶体数据文件可从网上获得,Display Style,设置原子、蛋白质、核酸显示模式,Windows-New Hierarchy Window,可打开蛋白质、核酸序列的窗口，可选择显示底物和受体,六、,POV-Ray,绘制分子,3D,图,camera ,orthographic,location ,right -4/3*x,angle 50.000000,look_at ,light_source rgb parallel point_at ,light_source, rgb parallel point_at ,background color rgb ,object ,#declare _WLVP_line_width = 0.02;,#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,union ,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,finish diffuse 0.9 ambient 0 specular 0.4 roughness 0.2 ,finish diffuse 0.9 ambient 0 specular,0.74,roughness,0.002,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 parallel 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, 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 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*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 ,# declare MOL=,union ,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 , 0.348750 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 , 0.247500 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 , 0.247500 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 ,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 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 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 ,union,union,unionMOL rotate,unionC3 rotate,unionC2 rotate,unionC2 rotate,unionC2 rotate,box , hollow on pigmentrgbt interior ior 1.55 rotate no_shadow finishFGlass ,box , hollow on pigmentrgbt interior ior 1.55 rotate no_shadow finishFGlass ,box , hollow on pigmentrgbt interior ior 1.55 rotate no_shadow finishFGlass ,rotate,rotate,scale Scale,sphere ,200 pigment rgb scale x*10 finish diffuse 0.2 ambient 0.2 specular 0.9 roughness 0.001 ,text ttf timesi.ttf sunhw 0.1,0 pigment rgbt finish FMetal scale 2 rotate translate ,