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import py3Dmol import glob import matplotlib.pyplot as plt from colabfold.colabfold import plot_plddt_legend from colabfold.colabfold import pymol_color_list, alphabet_list rank_num = 1 #["1", "2", "3", "4", "5"] color = "lDDT" # ["chain", "lDDT", "rainbow"] show_sidechains = True show_mainchains = True tag = results["rank"][0][rank_num - 1] jobname_prefix = ".custom" if msa_mode == "custom" else "" pdb_filename = f"{jobname}/{jobname}{jobname_prefix}_unrelaxed_{tag}.pdb" pdb_file = glob.glob(pdb_filename) def show_pdb(rank_num=1, show_sidechains=False, show_mainchains=False, color="lDDT"): model_name = f"rank_{rank_num}" view = py3Dmol.view(js='https://3dmol.org/build/3Dmol.js',) view.addModel(open(pdb_file[0],'r').read(),'pdb') if color == "lDDT": view.setStyle({'cartoon': {'colorscheme': {'prop':'b','gradient': 'roygb','min':50,'max':90}}}) elif color == "rainbow": view.setStyle({'cartoon': {'color':'spectrum'}}) elif color == "chain": chains = len(queries[0][1]) + 1 if is_complex else 1 for n,chain,color in zip(range(chains),alphabet_list,pymol_color_list): view.setStyle({'chain':chain},{'cartoon': {'color':color}}) if show_sidechains: BB = ['C','O','N'] view.addStyle({'and':[{'resn':["GLY","PRO"],'invert':True},{'atom':BB,'invert':True}]}, {'stick':{'colorscheme':f"WhiteCarbon",'radius':0.3}}) view.addStyle({'and':[{'resn':"GLY"},{'atom':'CA'}]}, {'sphere':{'colorscheme':f"WhiteCarbon",'radius':0.3}}) view.addStyle({'and':[{'resn':"PRO"},{'atom':['C','O'],'invert':True}]}, {'stick':{'colorscheme':f"WhiteCarbon",'radius':0.3}}) if show_mainchains: BB = ['C','O','N','CA'] view.addStyle({'atom':BB},{'stick':{'colorscheme':f"WhiteCarbon",'radius':0.3}}) view.zoomTo() return view show_pdb(rank_num, show_sidechains, show_mainchains, color).show() if color == "lDDT": plot_plddt_legend().show()