chain c. Chain-identifier-list单字母或有时是数字PyMOL>select 007,chain a segi s. Segment-identifier-list至多4字母PyMOL>select ligand,segi lig flag f. Flag-number从0到31的单整数PyMOL>select f1,flag 0 numeric_type nt. Type-number单整数PyMOL>select f1,nt. 5 text_type tt. Type-string至...
PyMOL select ligand, active around 3.5 and resn FMT PyMOL show sticks, ligand PyMOL show spheres, ligand 43 PyMOL alter ligand, vdw=0.5 PyMOL rebuild PyMOL set trans 16、parency=0.25 8. Rendering and output PyMOL bg_color white PyMOL ray File - Save Image 44 活性位点侧链显示及距离...
{pdb_name}') #label neighbor residues in receptor around ligand neighbor_res = f'{pdb_name} and (byres ({lig_name} around 4))' neighbor_res_ca = f'{neighbor_res} and name CA' cmd.select(f'res_ca_{pdb_name}', neighbor_res_ca) cmd.label(f'res_ca_{pdb_name}', 'oneletter+...
Color the active site residue PyMOL> select active, (resi 14-20,38 and chain A) PyMOL> color yellow, active PyMOL> turn y, -60; turn x, -20 PyMOL> zoom active Locate and display the bound formate ion in the active site. PyMOL> select ligand, active around 3.5 and resn FMT Py...
[return to KB Wong's home page]Through this tutorial, you will be able to generate the following figures:You can download the files for the tutorials here Files included:1w2i.pdb - crystal structure of PH acylphosphatase (PDB: 1W2I) (2fofc.map.xplor - electron density map from CNS/...
PyMOL> select active, (resi 14-20,38 and chain A) PyMOL> color yellow, active PyMOL> turn y, -60; turn x, -20 PyMOL> zoom active Locate and display the bound formate ion in the active site. PyMOL> select ligand, active around 3.5 and resn FMT ...
list单字母PyMOL>selectaltconf,alta+’‘chainc.Chain-identifier-list单字母或有时是数字PyMOL>select007,chainasegis.Segment-identifier-list至多4字母PyMOL>selectligand,segiligflagf.Flag-number从0到31的单整数PyMOL>selectf1,flag0numeric_typent.Type-number单整数PyMOL>selectf1,nt.5Text_typett.Type-...
select("ligand","organic") cmd.save("ligs.sdf","ligand") cmd.quit() 一个pdb文件中有2个小分子,希望保存成sdf数据库,该数据库中有1个小分子包含2个片段,则使用create+save组合。 示例代码: from pymol import cmd cmd.delete("all") cmd.load("target.pdb") cmd.load("receptor.pdb") cmd....
(甲酸盐离子)并将配体显示成球形 select ligand,resn FMT;color cyan, ligand; 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...
select selection-name,selection-expression 例如 PyMOL>select boy007,resi 1-10 #选择残基并命名为“boy007” 然后使用这个名称: 语法 zoom selection-name hide representation,selection-name show representation,selection-name 例如 PyMOL>zoom boy007