[modeller_usage] Advice on Modeller usage

["Nagesh Chakka" <>]

Hi,
I am trying to use Modeller to obtain a model using the structure 1XU0.
I have created the three files needed for Modeller

Atom file
http://www.rcsb.org/pdb/navbarsearch.do?newSearch=yes&isAuthorSearch=no&radioset=All&inputQuickSearch=1xu0&image.x=0&image.y=0&image=Search

Alignment file

>P1;1XU0
structureX:1XU0:125:A:226:A::::
IGGYMLGNAVGRMSYQFNNPMESRYYNDYYNQMPNRVYRPMYRGEEYVSEDRFVRDCYNM
SVTEYIIKPAEGKNNSELNQLDTTVKSQIIREMCITEYRRGS
*
>P1;XlPrP2
sequence:XlPrP2:1::134:::::
IGGYMLGNAVGRMNHHFDNPMESRYYNDYYNQMPDRVYRPMYRSEEYVSEDRFVTDCYNM
SVTEYIIKPSEGKNGSDVNQLDTVVKSKIIREMCITEYRRGS

Top file

INCLUDE

SET OUTPUT_CONTROL = 1 1 1 1 1
SET ALNFILE = 'inputAlignment_files/prp2StructAli.txt'
SET KNOWNS = '1XU0'
SET SEQUENCE = 'XlPrP2'
SET ATOM_FILES_DIRECTORY = '/home/nagesh/modelling/structure'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 4

CALL ROUTINE = 'model'

In doing so, the final model XlPrP2.B99990004 does not contain all the
atoms for a particular residue.

For example, the following is the part of the model for one amino acid

ATOM      1  N   ILE     1      14.910   4.779   7.839  1.00 41.08      
1SG   2
ATOM      2  CA  ILE     1      13.848   4.061   8.581  1.00 41.08      
1SG   3
ATOM      3  CB  ILE     1      12.918   3.371   7.630  1.00 41.08      
1SG   4
ATOM      4  CG2 ILE     1      11.924   2.529   8.447  1.00 41.08      
1SG   5
ATOM      5  CG1 ILE     1      12.242   4.416   6.730  1.00 41.08      
1SG   6
ATOM      6  CD1 ILE     1      11.473   3.813   5.557  1.00 41.08      
1SG   7
ATOM      7  C   ILE     1      14.422   3.050   9.510  1.00 41.08      
1SG   8
ATOM      8  O   ILE     1      15.261   2.235   9.128  1.00 41.08      
1SG   9

Atoms from the structure file

ATOM      1  N   ILE A 125      15.197  -5.772  -0.208  1.00  0.00        
  N
ATOM      2  CA  ILE A 125      14.432  -5.479   0.993  1.00  0.00        
  C
ATOM      3  C   ILE A 125      14.890  -6.453   2.086  1.00  0.00        
  C
ATOM      4  O   ILE A 125      14.874  -7.667   1.884  1.00  0.00        
  O
ATOM      5  CB  ILE A 125      12.922  -5.586   0.661  1.00  0.00        
  C
ATOM      6  CG1 ILE A 125      12.526  -4.523  -0.390  1.00  0.00        
  C
ATOM      7  CG2 ILE A 125      12.073  -5.416   1.930  1.00  0.00        
  C
ATOM      8  CD1 ILE A 125      11.131  -4.703  -1.000  1.00  0.00        
  C
ATOM      9  H   ILE A 125      14.783  -6.386  -0.892  1.00  0.00        
  H
ATOM     10  HA  ILE A 125      14.656  -4.459   1.305  1.00  0.00        
  H
ATOM     11  HB  ILE A 125      12.723  -6.575   0.246  1.00  0.00        
  H
ATOM     12 1HG1 ILE A 125      12.591  -3.543   0.075  1.00  0.00        
  H
ATOM     13 2HG1 ILE A 125      13.228  -4.540  -1.223  1.00  0.00        
  H
ATOM     14 1HG2 ILE A 125      12.338  -4.494   2.447  1.00  0.00        
  H
ATOM     15 2HG2 ILE A 125      11.014  -5.400   1.691  1.00  0.00        
  H
ATOM     16 3HG2 ILE A 125      12.237  -6.268   2.586  1.00  0.00        
  H
ATOM     17 1HD1 ILE A 125      10.989  -3.972  -1.797  1.00  0.00        
  H
ATOM     18 2HD1 ILE A 125      11.032  -5.707  -1.414  1.00  0.00        
  H
ATOM     19 3HD1 ILE A 125      10.362  -4.542  -0.250  1.00  0.00        
  H

What is the reason for the loss of the atoms and how can I fix this.
Thank you very much in advance
Nagesh