Install

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conda create -n 'pymol' python=3.9
conda activate 'pymol'

# 下载相应包后，用该环境下的python进行安装
D:\Anaconda\envs\'pymol'\python.exe -m pip install D:/pymolpack/numpy-1.22.4+vanilla-cp39-cp39-win_amd64.whl

D:\Anaconda\envs\'pymol'\python.exe -m pip install D:/pymolpack/pymol-2.6.0a0-cp39-cp39-win_amd64.whl

D:\Anaconda\envs\'pymol'\python.exe -m pip install D:/pymolpack/pymol_launcher-2.5-cp39-cp39-win_amd64.whl

D:\Anaconda\envs\'pymol'\python.exe -m pip install D:/pymolpack/Pmw-2.0.1-py3-none-any.whl

pip install PyQt5
  • 之后在D:\Anaconda\envs'pymol’ 下 打开pymol

Use

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def generate(input_str):
    '''
    input_str = '[4,8]'
    return [4,5,6,7,8]
    '''
    input_list = ast.literal_eval(input_str)
    res = []
    for sublist in input_list:
        res += [i for i in range(sublist[0], sublist[1]+1)]
    return res


def show(num):
    exm_p = name[num]
    exm_i = index[num]
    exm_p_dir = os.path.join(pdb_dir, exm_p+'.pdb')
    save_dir = '/data/lwb/data/HumanProteins/View'

    pc.load(exm_p_dir)
    pc.hide('everything')
    pc.color('gray')
    pc.bg_color('white')

    pc.show('cartoon')
    pc.set('cartoon_transparency', 0.5)

    sel = '+'.join([str(i) for i in generate(exm_i)])
    print(sel)
    pc.select('cluster1', "resi "+sel)
    pc.show('cartoon', 'cluster1')
    pc.color('red', 'cluster1')

    pc.save(os.path.join(save_dir, exm_p+'.pse'))
    print(f"file saves in {os.path.join(save_dir, exm_p+'.pse')}")