4. cmd.find_pairs() 5. cmd.load() 6. cmd.create() 7. cmd.save() 8. cmd.delete() 9. cmd.get_chains() 10. cmd.select() 11. cmd.identify() 12. cmd.alter() 13. cmd.iterate() 14. cmd.extend() 写在前面:后面会根据学习情况不断更新文章~~ Pymol是操作像蛋白,RNA之类的大分子专...
Pymol是一款经常用于蛋白质结构可视化的软件,可以帮助研究者更好地理解蛋白质结构及其功能。在蛋白质结构中,氢键和二硫键是重要的相互作用,这些相互作用可以影响蛋白质的稳定性和结构。在Pymol中,我们可以使用一些命令来可视化氢键和二硫键。例如,使用“find_pairs hbond”命令可以找到氢键,并使用“show sticks, hbonds...
mode=float(mode)# ensure only N and O atoms are in the selectionselection = selection +" & e. n+o"ifnotselection2: hb = cmd.find_pairs(selection,selection,mode=mode,cutoff=cutoff,angle=angle)else: selection2 = selection2 +" & e. n+o"hb = cmd.find_pairs(selection,selection2,mode=...
set cartoon_discrete_colors, 1 or from the the “Cartoon” menu of the external GUI find “Discrete Colors” as the last item in the menu. Robert Campbell Color by atom type from a script The “util” module contains a number of functions that color the atoms according to type, with di...
As mentioned previously, all PyMol commands are covered by the Python API. And there are additional functions supported only in the API, not in the command line interface. Here is a list of those API only functions: cmd.exp_path cmd.extend cmd.extendaa cmd.find_pairs cmd.get_atom_coords...
⽤PyMOL展⽰配体和受体相互作⽤的原⼦和氢键 为了简化展⽰过程，我们设计了⼀个pml脚本 (脚本内有很详细的解释)，只需要修改脚本⾥⾯受体和配体的名字，然后在PyMOL的命令⾏界⾯输⼊PyMOL> run display.pml即可获得展⽰结果。当然这个脚本也可以使⽤程序generatePmlForHbond.py⽣成。### ...
select_distances, cmd.find_pairs, cmd.get_raw_alignment ''' from chempy import cpv state, quiet = int(state), int(quiet) if state < 1: state = cmd.get_state() valid_names = cmd.get_names_of_type('object:measurement') if names == '': names = ' '.join(valid_names) else: fo...
NAHydrated sodium cation bound in major groove of a 16-mer RNA of Watson-Crick base pairs. T4LWT T4 lysozyme as ribbon diagram (1.08 Ang): 3FA0. U816-mer dsRNA with 8 contiguous Us. U-helix RNA (1.37 Ang): 3nd3. WC816-mer dsRNA, Watson-Crick helix RNA: 3nd4. ...
NAHydrated sodium cation bound in major groove of a 16-mer RNA of Watson-Crick base pairs.水合钠阳离子结合在 Watson-Crick 碱基对的 16 聚体 RNA 的主要槽中。 T4LWT T4 lysozyme as ribbon diagram (1.08 Ang):3FA0. WT T4 溶菌酶作为带状图(1.08 Ang):3FA0。
Find and fix vulnerabilities Codespaces Instant dev environments GitHub Copilot Write better code with AI Code review Manage code changes Issues Plan and track work Discussions Collaborate outside of code Explore All features Documentation GitHub Skills ...