PyMOL软件使用示例.PDFVIP

PyMOL软件使用示例 报告人：常玉珊 组员：金淑娟、李娅娅、张录录 组号：G06 2013-06-21 PyMOL简介 • PyMOL (Python molecule) • 主要功能：创作高品质的小分子或是生物 大分子（特别是蛋白质）的三维结构图像。 • 网站：/ PyMOL 功能 • 读取多种文件格式(.pdb, .xyz, .mol2...) • 读取电子密度图(.ccp4 或xplor格式) • 可拓展的界面程序/python语言 • 将screen 存为图片文件(.png格式) • 会话保存/session save • 结构比对 • 测量：距离、角度、二面角 • 立体效果 • 光线追踪/ray • 探测静电力学 • 动画制作 • • 没有undo功能 PyMOL界面 External GUI window command line：Ctrl-C/X/V Viewer window Object list Mouse Mode command line Movie player Settings PyMol has over 600 settings! Everything from ray tracing fog, to perspective viewing, stereo rendering, colors, textures, memory settings and many more! 实例演示 以胰岛素(PDB:4INS)为例 1. Load the PDB file •File Open 4INS.pdb •load ../4INS.pdb •Displaysequence or 单击右下角“s ”按钮#显示序列(4条链, 2 ZN) 2. show/hide different representation •Show ascartoon •hide everything, all •show cartoon, all • 鼠标L/M/R键示例 3. Color the helix, sheet, and loop •color by ss Helix Sheet Loop •color by chain chainbows #用于观察链的走向 •color red , ss h •color yellow, ss s •color green, ss 4. Color chain A and B •color blue, chain A color red, chain B 5. Create a surface display for chain A and chain B •create obj_ab, chain A or chain B •show surface, obj_ab 6. Find and Color the active site residue select zn, resn ZN and obj_ab showspheres, zn alter zn, vdw=1.3 rebuild •select active, zn around 10.0 and obj_ab •color yellow, active •set transparency=0.25 •zoom active •orient active 7. Rendering and output •bg_color white •ray •File Save Image 8.Display the side-chain of a