PyMOL>select boy,resi 1+2+3 #残基1、2和3被选择 PyMOL>select 007,resi 1-10 #残基1到10被选择 谨记在同一标识符后不可同时出现“+”“-”,如“select bad,resi 1-4+9”。 对于空白数据区,标识符是一对空的双引号: PyMOL>select blank,ss “” #blank包含非二级结构的所有原子 大多数的属性选...
当创建一个selection-name后,PYMOL会在控制面板显示出,以便利用面板里的控制功能(见“PYMOL命令”)。 命名的选择(named-selection)如“boy007”和PYMOL的对象(object)是有本质区别的。当载入文件时PYMOL创建object-name用来盛放数据,而选择是指向一组数据的方式。为了区别selection-names和object-names,在控制面板里s...
select hydrophobes,(resn ala+gly+val+ile+leu+phe+met+pro+trp) show sticks, (interface and hydrophobes and (!name c+n+o)) 分两步,首先找到相互作用界面,其次选中疏水氨基酸并展示侧链。 1、InterfaceResidues - PyMOLWiki,去这个网址下载脚本,InterfaceResidues.py。 先运行脚本,操作如下 File → Ru...
color blue, LdonPacc#distance Fe_C20, (fep and name C20), (heme and name fe))# The following 6 lines:# 1. Select non-hydro atoms of ligands# 2. Select protein atoms within 5A of selected atoms in last step# 3. Label alpha-c(ca) of selected residues with residue name and residue...
的所有原子PyMOL>selectfarfrm_ten,resi10gap5s1aroundxs1a.x选择中心在以s1任何原子为中心,以x埃为半径的范围内的所有原子PyMOL>selectnear_ten,resi10around5s1expandxs1e.x通过在以s1任何原子为中心,以x埃为半径的范围内的所有原子扩充s1PyMOL>selectnear_ten_x,near10expand3s1withinxofs2s1w.xofs2选择...
select b, ///B/229/Ndistance d, a, bThis will give you a dashed line object d which is labelled with the distance between the twoatoms ‘a’ and ‘b’ - you can get rid of the label usinghide labels, dbtw, if you want to ray-trace the image, I find the dashes come out a...
Display the side-chain of active site residues on top of the cartoon representation ? PyMOL hide surface ? PyMOL select sidechain, not (name c+n+o) ? PyMOL show sticks, (active and sidechain) ? PyMOL color blue, name n* ? PyMOL color red, name o* ? PyMOL color white, name c...
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。 上面的图看起来有点乱,因为默认Pymol在每个原子上都打上了标签。要想看起来顺眼点,需要一点加工。 在...
matchalign: aligning residues (349 vs 66). executivealign: 47 atoms a 18、ligned. executive: rms = 12.490 (47 to 47 atoms)静电势apbs(目前没有大问题)各种静电势方法总结delphi+pymol做出来的图和apbs+pymol的有区别,iqcg的iq用两种方法做出来的图,apbs法做的和单用pymol的都有尾部红色区(后者...
#distance Fe_C20, (fep and name C20), (heme and name fe))# The following 6 lines:# 1. Select non-hydro atoms of ligands # 2. Select protein atoms within 5A of selected atoms in last step # 3. Label alpha-c(ca) of selected residues with residue name and residue position # 4. ...