[modeller_usage] protein 3 D structure alignment

["drugdesign" <>]

Dear modeller users,
I have a series of 3D structures built by MODELLER. I need top make 3D alignment of these  structures because  I need to see the differences between these protein stuctures (they are from one family of proteins) and the RMSD from RMS coordinates of the proteins. Which scrip is better  to use for it? There are 2  MODELLER scripts below. Where in these scripts  I need  to put my PDB files. Fpr example I have prot1.pdb, rpot2.pdb and prot3.pdb and 1-3.ali file. How such script must look with these files?
Respectively yours,
Andrew
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# Illustrates the SALIGN multiple structure/sequence alignment

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

aln = alignment(env)
for (code, chain) in (('1is4', 'A'), ('1uld', 'D'), ('1ulf', 'B'),
                      ('1ulg', 'B'), ('1is5', '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_cutoffs=(3.5, 6., 60, 60, 15, 60, 60, 60, 60, 60, 60),
               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='1is3A.tree',
               alignment_type='tree', # If 'progresive', the tree is not
                                      # computed and all structues will be
                                      # aligned sequentially to the first
               #ext_tree=True,        # Tree building can be avoided if the tree
                                      # is input
               #input_weights_file='1is3A_exmat.mtx',
               feature_weights=weights, # For a multiple sequence alignment only
                                        # the first feature needs to be non-zero
               improve_alignment=True, fit=True, write_fit=write_fit,
               write_whole_pdb=whole, output='ALIGNMENT QUALITY')

aln.write(file='1is3A.pap', alignment_format='PAP')
aln.write(file='1is3A.ali', alignment_format='PIR')

# The number of equivalent positions at different RMS_CUTOFF values can be
# computed by changing the RMS value and keeping all feature weights = 0
aln.salign(rms_cutoffs=(1.0, 6., 60, 60, 15, 60, 60, 60, 60, 60, 60),
           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='1is3A.tree',
           alignment_type='progressive', feature_weights=[0]*6,
           improve_alignment=False, fit=False, write_fit=True,
           write_whole_pdb=False, output='QUALITY')