根据Modeller官网教程2进行建模（多模版、环、配体）

Tutorial Advanced Modeling
https://salilab.org/modeller/tutorial/advanced.html

为了提高模型的准确性，可采用三种方法：

• Use of multiple templates
• Modeling the loop using ab-initio methods
• Modeling using a known ligand bound to the binding site

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多模版

1bdm属于fm00495家族，有4个成员：2mdh:A, 2mdh:B. 1b8p:A and 1bdm:A
可用salign()来建立该家族的multiple structure alignment

• salign.py 用于多模版对齐

# Illustrates the SALIGN multiple structure/sequence alignment

from modeller import *

log.verbose()
env = environ()
env.io.atom_files_directory = './:../atom_files/'

aln = alignment(env)
for (code, chain) in (('2mdh', 'A'), ('1bdm', 'A'), ('1b8p', 'A')):
    mdl = model(env, file=code, model_segment=('FIRST:'+chain, 'LAST:'+chain))
    aln.append_model(mdl, atom_files=code, align_codes=code+chain)

for (weights, write_fit, whole) in (((1., 0., 0., 0., 1., 0.), False, True),
                                    ((1., 0.5, 1., 1., 1., 0.), False, True),
                                    ((1., 1., 1., 1., 1., 0.), True, False)):
    aln.salign(rms_cutoff=3.5, normalize_pp_scores=False,
               rr_file='$(LIB)/as1.sim.mat', overhang=30,
               gap_penalties_1d=(-450, -50),
               gap_penalties_3d=(0, 3), gap_gap_score=0, gap_residue_score=0,
               dendrogram_file='fm00495.tree',
               alignment_type='tree', # If 'progresive', the tre