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Re: [modeller_usage] alignment file!

You need the same fields for your sequence as your template
P1;1EBV
sequence:1EBV:starting residue:chain:ending residue:chain::::

VNPCCYYPCQHQGICVRFGLDRYQCDCTRTGYSGPNCTIPEIWTWLRTTLRPSPSFIHF
LLTHGRWLWDFVNATFIRDTLMRLVLTVRSNLIPSPPTYNIAHDYISWESFSNVSYYTRI
LPSVPRDCPTPMGTKGKKQLPDAEFLSRRFLLRRKFIPDPQGTNLMFAFFAQHFTHQFFK
TSGKMGPGFTKALGHGVDLGHIYGDNLERQYQLRLFKDGKLKYQMLNGEVYPPSVEEAPV
LMHYPRGIPPQSQMAVGQEVFGLLPGLMLYATIWLREHNRVCDLLKAEHPTWGDEQLFQT
ARLILIGETIKIVIEEYVQQLSGYFLQLKFDPELLFGAQFQYRNRIAMEFNQLYHWHPLM
PDSFRVGPQDYSYEQFLFNTSMLVDYGVEALVDAFSRQPAGRIGGGRNIDHHILHVAVDV
IKESRVLRLQPFNEYRKRFGMKPYTSFQELTGEKEMAAELEELYGDIDALEFYPGLLLEK
CHPNSIFGESMIEMGAPFXLKGLLGNPICSPEYWKASTFGGEVGFNLVKTATLKKLVCLN
TKTCPYVSFHVP*


 in the file my.ali and erase the '-'s.

On Thursday, May 6, 2004, at 08:27  PM, Yue Yun wrote:


Hello everyone,

I got the following error message when Modeller  reads my alignment
file:
rdpir___270E> Error reading/processing file:  my.ali
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Here's my input file:

P1;1Q4G

structureX:1Q4G:32:A:584:A::::
PVNPCCYYPCQHQGICVRFGLDRYQCDCTRTGYSGPNCTIPEIWTWLRTTLRPSPSFIHF
LLTHGRWLWDFVNATFIRDTLMRLVLTVRSNLIPSPPTYNIAHDYISWESFSNVSYYTRI
LPSVPRDCPTPMGTKGKKQLPDAEFLSRRFLLRRKFIPDPQGTNLMFAFFAQHFTHQFFK
TSGKMGPGFTKALGHGVDLGHIYGDNLERQYQLRLFKDGKLKYQMLNGEVYPPSVEEAPV
LMHYPRGIPPQSQMAVGQEVFGLLPGLMLYATIWLREHNRVCDLLKAEHPTWGDEQLFQT
ARLILIGETIKIVIEEYVQQLSGYFLQLKFDPELLFGAQFQYRNRIAMEFNQLYHWHPLM
PDSFRVGPQDYSYEQFLFNTSMLVDYGVEALVDAFSRQPAGRIGGGRNIDHHILHVAVDV
IKESRVLRLQPFNEYRKRFGMKPYTSFQELTGEKEMAAELEELYGDIDALEFYPGLLLEK
CHPNSIFGESMIEMGAPFSLKGLLGNPICSPEYWKASTFGGEVGFNLVKTATLKKLVCLN
TKTCPYVSFHVPD*

P1;1EBV

sequence
-VNPCCYYPCQHQGICVRFGLDRYQCDCTRTGYSGPNCTIPEIWTWLRTTLRPSPSFIHF
LLTHGRWLWDFVNATFIRDTLMRLVLTVRSNLIPSPPTYNIAHDYISWESFSNVSYYTRI
LPSVPRDCPTPMGTKGKKQLPDAEFLSRRFLLRRKFIPDPQGTNLMFAFFAQHFTHQFFK
TSGKMGPGFTKALGHGVDLGHIYGDNLERQYQLRLFKDGKLKYQMLNGEVYPPSVEEAPV
LMHYPRGIPPQSQMAVGQEVFGLLPGLMLYATIWLREHNRVCDLLKAEHPTWGDEQLFQT
ARLILIGETIKIVIEEYVQQLSGYFLQLKFDPELLFGAQFQYRNRIAMEFNQLYHWHPLM
PDSFRVGPQDYSYEQFLFNTSMLVDYGVEALVDAFSRQPAGRIGGGRNIDHHILHVAVDV
IKESRVLRLQPFNEYRKRFGMKPYTSFQELTGEKEMAAELEELYGDIDALEFYPGLLLEK
CHPNSIFGESMIEMGAPFXLKGLLGNPICSPEYWKASTFGGEVGFNLVKTATLKKLVCLN
TKTCPYVSFHVP-*

Here's my .top file:
# Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines 

SET OUTPUT_CONTROL = 1 1 1 1 1      # uncomment to produce a large log
file
SET ALNFILE  = 'my.ali'      # alignment filename
SET KNOWNS   = '1Q4G'               # codes of the templates
SET SEQUENCE = '1EBV'               # code of the target
SET ATOM_FILES_DIRECTORY = './:../atom_files' # 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
Can anyone help me to solve this question? I download the 1Q4G.pdb file 
from the www.pdb.org.

Thank you!


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