[modeller_usage] Problem with PDB file

30 Jun 2004


      Dear colleagues,
I�m facing a problem with Modeller6, and although it
seems to be a common one (I�ve seen similar requests
in the list archives), I just couldn�t fix it reading
the previous posts nor the FAQ.
The PDB file I�m using as a template starts at residue
8 and ends at residue 315. So, my alignement is as
follows:
=======================================================
C; A sample alignment in the PIR format; used in
tutorial
>P1;1DKU
structureX:1DKU:8    : :315  : :PRPP:bacilo: 1.90:
0.19
NLKIFSLNSNPELAKEIADIVGVQLGKCSVTRFSDGEVQINIEESIRGCDCYIIQSTSDPVNEHIMELLIMVDALKRASAKTINIVIPYYGY
ARQDRKARSREPITAKLFANLLETAGATRVIALDLHAPQIQGFFDIPIDHLMGVPILGEYFEGKNLE--DIVIVSPDHGGVTRARKLADRLKAPIAIIDK
RRPRPNVAEVMNIVGNIEGKTAILIDDIIDTAGTITLAANALVENGAKEVYACCTHPVLSGPAVERINNSTIKELVVTNSIKLPEEKK-IERFKQLSVGP
LLAEAIIRVHEQQSVSYLFS----*
>P1;HUMA
sequence:HUMA:8    : :315   : :PRPP:Homo sapiens:
2.00:-1.00
NIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEINDNLMELLIMINACKIASASRVTAVIPCFPY
ARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDIPVDNLYAEPAVLKWIRENISEWRNCTIVSPDAGGAKRVTSIADRLNVDFALIHK
ERKKANEVDRMVLVGDVKDRVAILVDDMADTCGTICHAADKLLSAGATRVYAILTHGIFSGPAISRINNACFEAVVVTNTIPQEDKMKHCSKIQVIDISM
ILAEAIRRTHNGESVSYLFSHVPL*
=======================================================
The .top file was directly edited from the example
model-default.top, and is as follows:
======================================================
# Homology modelling by the MODELLER TOP routine
'model'.
INCLUDE                             # Include the
predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 2      # uncomment to
produce a large log file
SET ALNFILE  = 'ALIN.pir'      # alignment filename
SET KNOWNS   = '1DKU'               # codes of the
templates
SET SEQUENCE = 'HUMA'               # code of the
target
SET ATOM_FILES_DIRECTORY =
'/mod6v2/examples/tutorial-model/' # directories for
input atom files
SET STARTING_MODEL= 1               # index of the
first model 
SET ENDING_MODEL  = 1               # index of the
last model
                                    # (determines how
many models to calculate)
CALL ROUTINE = 'model'              # do homology
modelling
=====================================================
Both the alignement file "ALIN.pir" and PDB file
"1DKU.pdb" are on the /mod6v2/examples/tutorial-model/
directory. But although the program actually opens
this pdb file, it shows this message:
rdabrk__288W> Protein not accepted:        1
rdabrk__290E> Number of residues in the alignment and 
pdb files are different:
     309        0
              For alignment entry:        1
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1 
     1
Does anybody has any hint on how to fix this problem?
Thanks in advance,
Lucas Bleicher
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