[BiO BB] Advice on using Modeller

Mon Mar 6 00:58:50 EST 2006

Dear Nagesh

  You can do it again as well as use the other sequences to check this problemb.

  Good luck,

Nagesh Chakka <nagesh.chakka at anu.edu.au> wrote:
  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

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Nguyen Xuan Hung

Institute of Biologycal and Food Technology
HaNoi University of Technology
No.1 Dai Co Viet
VietNam

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