pymol常用命令
select sheet, (ss s)select loop, (ss l+’’)Color by atom type from a scriptThe “util” module contains a number of functions that color the atoms according to type, withdifferent colors for the C atoms. For instance,util.cbay threein a .pml script will color object “three” by ...
show surface, 1hpv show cartoon, chain b show spheres, 1vgc and resi 95 color yellow, name ca zoom - 用于将视图集中在特定原子上 zoom resi 110-120 zoom all label - 用于创建标签 label name ca, resn+resi label 1hpv//B/25/CG, "Active Site" label solvent, "%1.1f"%b select - 用于...
Command Completion using TAB If you type the first few characters of a command and then hit TAB...
选择分子部分:使用select命令选择特定原子,如select protein, chain A。 显示和隐藏:使用show和hide命令来显示或隐藏分子组件,如show cartoon显示卡通样式。 颜色设置:使用color命令为分子组件着色,如color red, protein将蛋白质链设置为红色。 高级功能 光线追踪:使用ray命令或点击“Ray Trace”按钮,可以制作出最高质量...
PyMOL简介及相关操作
22、; show sticks, ligand show spheres, ligand 4.改变球形直径大小,并将表面透明度设成0.25 alter ligand, vdw=0.5 rebuild set transparency=0.25 5.选择活性位点,并将活性位点的颜色显示成黄色, select active, ligand around 6.5 and chain A;color yellow, active zoom active PyMOL ray File - Save Ima...
Pymol> extract pro, chain a Pymol> delete tmp Pymol> select near, pro within 4.5 of upg Pymol> hide all Pymol> show sticks, upg Pymol> show lines, near Pymol> label near, ("%s/%s") % (resn, resi)#("%s/%s"):设定显示格式。
extract cha,chain a extract chb,chain b select near, cha within 4.5 of chb 从选择的原子扩展到残基 create pocket, byres 4dxd within 5 of resn 9pc (这条命令的目的就是以残基9pc为中心,在4dxd这个蛋白质里找出跟9pc距离在5 A的氨基酸,生成一个pocket, 9pc这个残基是4dxd这个蛋白质晶体中的一...
command to write out a PDB file containing the atom selection of interest You can then apply the system command to run molauto and molscript and then load the Raster3D file back into PyMOL save tmp pdb chain C system molauto nocentre tmp pdb molscript r tmp r3d load tmp r3d molauto ...