cmd.remove("resi 3") 2. cmd.h_add() (1) 加氢 cmd.h_add("6dh0_protein") 3. cmd.get_fastastr() (1) 获取蛋白残基序列信息 print(cmd.get_fastastr("3u7s_po")) (2) 获取蛋白中某条链的残基序列信息 print(cmd.get_fastastr("model 6A2B and chain C")) 4. cmd.find_pairs() ...
from pymol import cmd, cgo from pymol.cgo import * import numpy from random import randint def matriz_inercia(selection): model = cmd.get_model(selection) totmass = 0.0 x,y,z = 0,0,0 for a in model.atom: m = a.get_mass() x += a.coord[0]*m y += a.coord[1]*m z +=...
2.输入指令select protein, residue 1-317 ##residue1-317 改成你需要分析的蛋白的氨基酸残基数,即读取要分析的蛋白的氨基酸数 3.输入指令open("ss-test.txt","w").writelines( ["Residue %s: %s\n"%(a.resi,a.ss) for a in cmd.get_model("protein" +" and n. ca").atom] ) ##ss-test.txt...
PyMOL>load $PyMOL_path/test/dat/pept.pdb 命令输入后,PYMOL会打开读取“pept.pdb”,创建并命名相应的对象,在Viewer中显示图像并在控制板中添加对象。 默认状态下,PYMOL会在文件读取后命名对象,当然也可以重命名对象: 语法 load data-file-name,object-name 例如 PyMOL>load $PyMOL_path/test/dat/pept.pdb...
get_model('sele').atom[0].coord) Q19. pymol有没有命令返回在氨基酸编号,在小分子4A范围内氨基酸的编号? 这里以JAK1 (PDB ID:3EYG)为例, 示例代码如下: from pymol import cmd select mt1around5, name ca and byres (resn MI1 around 5 and polymer) and name ca atoms =cmd.get_model("mt1...
(.py 或.pym为扩展名)应用Python loop载入一系列编好号的PDB文件,然后配置PyMOL显示它们向前和向后: from glob import glob from PyMOL import cmd file_list = glob(“mov*.pdb”): for file in file_list cmd.load(file,“mov”) cmd.mset(“1 -%d -2”%len(file_list)) 预览ray-traced动画图片...
(.py或.pym为扩展名)应用Pythonloop载入一系列编好号的PDB文件,然后配置PyMOL显示它们向前和向后:fromglobimportglobfromPyMOLimportcmdfile_list=glob(“mov*.pdb”):forfileinfile_listcmd.load(file,“mov”)cmd.mset(“1-%d-2”%len(file_list))预览ray-traced动画图片PyMOL能够在RAM中缓存一系列图片,...
"""quiet=int(quiet)totmass=0.0ifmass!=Noneandnotquiet:print("Calculating mass-weighted COM")state=int(state)model=cmd.get_model(selection,state)x,y,z=0,0,0forainmodel.atom:if(mass!=None):m=a.get_mass()x+=a.coord[0]*m y+=a.coord[1]*m ...
= None and not quiet:print("Calculating mass-weighted COM")state = int(state)model = cmd.get_model(selection, state)x, y, z = 0, 0, 0for a in model.atom:if (mass != None):m = a.get_mass()x += a.coord[0] * my += a.coord[1] * mz += a.coord[2] * mtotmass +...
(pep)),quiet=1,mode=2,label=0,reset=1);cmd.enable(pep_polar_conts) 结构叠加比对 Align命令用法 Pymol can superpose two structures; type the following at the pymol command line: align mol1, mol2 先打开Ca复合物,然后选B,重命名为cb,再打开EDTA复合物,选择b链,在cb里选align to selection-...