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