《分子3D绘图》PPT课件

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,TeslaK808.74TFlopsv.s.BlueGene/L135.58.74TFlops,KnightsLandingXeonPhi3TFlops,E7-8890V424核,PerformanceDevelopment,Kcomputer2011.62012.5,Tianhe-1A2010.102011.5,Sequoia-BlueGene/Q2012.6-2012.10,Titan2012.112013.5,Tianhe-22013.62016.6,曾经的Top1,SunwayTaihuLight2016.6,48thTOP10November2016,中国有171台超级计算机入围TOP500,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,Thepredictionofthemolecularstructureofmoleculesbytheuseofthesimulationofforces,ormoreaccuratequantumchemicalmethods,tofindstationarypointsontheenergysurfaceasthepositionofthenucleiisvaried.Storingandsearchingfordataonchemicalentities(seechemicaldatabases).Identifyingcorrelationsbetweenchemicalstructuresandproperties(QSPR/QSAR).Computationalapproachestohelpintheefficientsynthesisofcompounds.Computationalapproachestodesignmoleculesthatinteractinspecificwayswithothermolecules(e.g.drugdesignandcatalysis).,1.4常用分子模拟软件,Gaussian98GaussView2.xGaussian03GaussView3.x,4.xGaussian09GaussView5.x,HyperChemProfessional8.010/GAMESS/PCGAMESS/Fireflyversion8.2.0http:/classic.chem.msu.su/gran/gamess/index.htmlNWChem6.6Free,MaterialsStudio图形计算平台，密度泛函，分子，溶剂，材料InsightII图形计算平台，生物分子SchrdingerSuite图形计算平台SYBYL图形计算平台,GROMACS5.1.4Free/,TINKER7.1Free/tinker/,AMBER16/,NAMD2.12Free/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DiscoveryStudioQSAR，图形用户界面,数据类型(最常见、纯文本格式)ENT/PDBBrookhavenProteinDataBankMOLMolecularDesign,Ltd.MDLHINHyperchemGJFGaussianMOL2TriposCIFCrystallographicInformationfile,二、分子3D结构数据,HETATM1CUNK11.2090.6980.000HETATM2CUNK11.209-0.6980.000HETATM3CUNK10.000-1.3970.000HETATM4CUNK1-1.209-0.6980.000HETATM5CUNK1-1.2090.6980.000HETATM6CUNK10.0001.3970.000HETATM7HUNK10.0002.4840.000HETATM8HUNK12.1511.2420.000HETATM9HUNK12.151-1.2420.000HETATM10HUNK10.000-2.4840.000HETATM11HUNK1-2.151-1.2420.000HETATM12HUNK1-2.1511.2420.000CONECT1628CONECT2139CONECT32410CONECT43511CONECT54126CONECT6175CONECT76CONECT81CONECT92CONECT103CONECT114CONECT125END,BEN.ENTBrookhavenPDB,BEN.GJFGaussian,%chk=H:ben.chk#B3LYP/6-31G*optBen01CC1B1C2B11AC3B12A1D1C4B13A2D1C1B12A3D1H1B26A5D2H2B21A6D2H3B22A1D2H4B23A2D2H5B24A3D2H6B21A2D2B11.40B21.08A120.D10.D2180.,BEN.GJFGaussian,%chk=H:ben2.chk#b3lyp/6-31g(d)opt=vtightBen01C0.000000000.000000000.00000000C0.000000000.000000001.39661073C1.209499370.000000002.09491637C2.419000480.000000001.39661228C2.419000480.000000000.00000155C1.209501110.00000000-0.69830409H-0.941384050.00000000-0.54350900H-0.941385380.000000001.94011906H1.209498900.000000003.18193419H3.360384530.000000001.94012127H3.360385860.00000000-0.54350678H1.209501580.00000000-1.78532191,C-0.25-0.470.00O-0.250.960.00H0.77-0.830.00H-0.77-0.830.89H-0.77-0.83-0.89H-1.161.280.00,内坐标输入(Z-Matrix),CC11.54H11.092109.47H11.092109.473-120.H11.092109.473120.H21.091109.473180.H21.091109.476-120.H21.091109.476120.,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,TheCambridgeCrystallographicDataCentre(CCDC)http:/www.ccdc.cam.ac.uk/CrystallographyOpenDatabase/TheWorldwideProteinDataBank/,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,MolekelRASMOL,VMD，MOLDEN,POVRAY先用分子模拟软件输出POV文件，再用POVRAY渲染,ViewerLite5.0,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ViewerPro4.2,6.0新版本DiscoveryStudio2016Client,.msv(Viewerbinaryfileformat.pdb.ent(BrookhavenProteinDataBank).mol.sdf.sd.mdl(MolecularDesign,Ltd.MDL).car(Accelrys,InsightII).csd.fdat.dat(CambridgeStructuralDatabaseCrystallographicfiles).mol2(Tripos).msf(Accelrys,QUANTA),.msi(Accelrys,Cerius2).cpd(Accelrys,Catalyst).chm(Accelrys,CatalystQuery).cif(CrystallographicInformationFile).xyz(generic).skc(MDL,ISIS).grd(Accelrys,InsightIIGridFile).wvc(ViewerCommandFile),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。,DiscoveryStudioClient,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,GaussView,商业软件配合Gaussian使用,Chem3D,商业软件使用广泛,ArgusLabAmolecularmodeling,graphics,anddrugdesignprogram,UCSFChimera,UCSFChimeraisahighlyextensibleprogramforinteractivevisualizationandanalysisofmolecularstructuresandrelateddata,includingdensitymaps,supramolecularassemblies,sequencealignments,dockingresults,trajectories,andconformationalensembles.High-qualityimagesandanimationscanbegenerated.,/chimera/,Molekelisanopen-sourcemulti-platformmolecularvisualizationprogram.,http:/ugovaretto.github.io/molekel/,VMD/Research/vmd/SupportforallmajorcomputerplatformsSupportformulticoreprocessorsSupportforGPUacceleratedcomputationGabedit,POVRAY绘制高水平3D图,POV-Ray，全名是PersistenceofVisionRaytracer，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。,/,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BuildAddH#declare_WLVP_dot_size=0.03;#declare_WLVP_text_depth=0.0;#declare_WLVP_text_scale=0.3;#declare_WLVP_finish=finishdiffuse0.9ambient0specular0.4roughness0.2,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FileSaveasPOV格式,unionsphere,0.290625translatepigmentrgbtfinish_WLVP_finishsphere,0.206250translatepigmentrgbtfinish_WLVP_finish.cylinder,0.090000pigmentrgbtfinish_WLVP_finishcylinder,0.090000pigmentrgbtfinish_WLVP_finishmatrixtranslatescale0.8,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,finishdiffuse0.9ambient0specular0.4roughness0.2,finishdiffuse0.9ambient0specular0.74roughness0.002,cameraorthographiclocationright-4/4*xangle90.0look_atlight_sourcergbparallelpoint_atlight_sourcergbparallelpoint_atshadowlesslight_sourcergbparallelpoint_atlight_sourcergbparallelpoint_atbackgroundcolorrgb#declareScale=5;#declareC3L=16/Scale;#declareC2L=16/Scale;#declareF=finishspecular0.4roughness0.005diffuse0.8ambient0.2#declareFGlass=finishspecular0.6roughness0.002ambient0.2diffuse0.8reflection0.2,0.5conserve_energy#declareFMetal=finishambient0.4brilliance2diffuse0.8metallicspecular0.90roughness0.002reflection0.1#declareC3T=objectprismlinear_sweeplinear_spline-0.025,/sweepthefollowingshapefromhere.0.025,/.upthroughhere4,/thenumberofpointsmakinguptheshape.,pigmentrgbtrotaterotatefinishFMetal/triangle#declareC3=unioncylinder,0.25/ScalepigmentrgbtfinishFMetalobjectC3Tscale7/ScaletranslateobjectC3Tscale7/Scaletranslaterotate#declareC2=unioncylinder,0.25/ScalepigmentrgbtfinishFMetalcylinder,0.2scalex*2rotaterotatescale2/ScaletranslatepigmentrgbtfinishFMetalcylinder,0.2scalex*2rotaterotatescale2/ScaletranslatepigmentrgbtfinishFMetal,#declareMOL=unionsphere,0.348750translatepigmentrgbtfinishFsphere,0.348750translatepigmentrgbtfinishFsphere,0.348750translatepigmentrgbtfinishFsphere,0.348750translatepigmentrgbtfinishFsphere,0.348750translatepigmentrgbtfinishFsphere,0.348750translatepigmentrgbtfinishFsphere,0.247500translatepigmentrgbtfinishFsphere,0.247500translatepigmentrgbtfinishFsphere,0.247500translatepigmentrgbtfinishFsphere,0.247500translatepigmentrgbtfinishFsphere,0.247500translatepigmentrgbtfinishFsphere,0.247500translatepigmentrgbtfinishFsphere,0.247500translatepigmentrgbtfinishFsphere,0.247500translatepigmentrgbtfinishFsphere,0.247500translatepigmentrgbtfinishFsphere,0.247500translatepigmentrgbtfinishFsphere,0.247500translatepigmentrgbtfinishFsphere,0.247500translatepigmentrgbtfinishFcylinder,0.06pigmentrgbtfinishFcylinder,0.06pigmentrgbtfinishFcylinder,0.06pigmentrgbtfinishFcylinder,0.06pigmentrgbtfinishFcylinder,0.06pigmentrgbtfinishFcylinder,0.06pigmentrgbtfinishFcylinder,0.06pigmentrgbtfinishFcylinder,0.06pigmentrgbtfinishFcylinder,0.06pigmentrgbtfinishFcylinder,0.06pigmentrgbtfinishFcylinder,0.06pigmentrgbtfinishFcylinder,0.06pigmentrgbtfinishFcylinder,0.06pigmentrgbtfinishFcylinder,0.06pigmentrgbtfinishFcylinder,0.06pigmentrgbtfinish