[modeller_usage] Error: No atoms were read from the specified input PDB file

[Ann Spevacek <>]

Hello -

I am trying to align two models, one an NMR structure (1XYX.pdb) and  
one a simulation (frame100.pdb) and I get the following error:

No atoms were read from the specified input PDB file, since the
              starting residue number and/or chain id in  
MODEL_SEGMENT (or
              the alignment file header) was not found;
              requested starting position: residue number " FIRST",  
chain " A";
              atom file name:  ./frame100.pdb

This is what the frame100.pdb file looks like:

REMARK    GENERATED BY TRJCONV
TITLE     Protein t=   2.00000
REMARK    THIS IS A SIMULATION BOX
CRYST1  183.372  183.372  183.372  60.00  60.00  90.00 P 1           1
MODEL        1
ATOM      1  N   LYS     1      85.750   9.110   4.370  1.00  0.00
ATOM      2  H1  LYS     1      84.780   9.360   4.220  1.00  0.00
ATOM      3  H2  LYS     1      86.050   8.430   3.680  1.00  0.00
ATOM      4  H3  LYS     1      85.790   8.630   5.260  1.00  0.00
ATOM      5  CA  LYS     1      86.670  10.260   4.390  1.00  0.00
ATOM      6  HA  LYS     1      86.750  10.670   3.380  1.00  0.00
ATOM      7  CB  LYS     1      86.190  11.350   5.350  1.00  0.00
ATOM      8  HB1 LYS     1      86.000  10.980   6.350  1.00  0.00
ATOM      9  HB2 LYS     1      86.920  12.120   5.570  1.00  0.00
ATOM     10  CG  LYS     1      84.950  12.080   4.820  1.00  0.00
ATOM     11  HG1 LYS     1      85.000  12.330   3.760  1.00  0.00
ATOM     12  HG2 LYS     1      84.170  11.340   4.990  1.00  0.00
....
ATOM   3050 HH12 ARG   206     120.270 -79.800 115.360  1.00  0.00
ATOM   3051  NH2 ARG   206     119.370 -82.100 116.310  1.00  0.00
ATOM   3052 HH21 ARG   206     118.870 -82.870 116.730  1.00  0.00
ATOM   3053 HH22 ARG   206     120.020 -81.560 116.870  1.00  0.00
ATOM   3054  C   ARG   206     120.920 -85.910 117.630  1.00  0.00
ATOM   3055  O1  ARG   206     121.830 -86.740 117.840  1.00  0.00
ATOM   3056  O2  ARG   206     119.950 -85.640 118.370  1.00  0.00
ATOM   3057  Zn  Zn2   207     171.290 -12.580  16.660  1.00  0.00
TER
ENDMDL


And this is the salign.py file that I am trying to use:

# 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 (('1XYX', 'A'), ('frame100', '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='PrP.tree',
               alignment_type='tree', # If 'progresive', the tree is  
not
                                      # computed and all structues  
will be
                                      # aligned sequentially to the  
first
               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='PrP.pap', alignment_format='PAP')
aln.write(file='PrP.ali', alignment_format='PIR')

aln.salign(rms_cutoff=1.0, 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')


Any input would be greatly appreciated!

Thanks!


Ann