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Alignment sequence not found in PDB file



Hi

I have problem in modeller(6v1). The error is "Alignment sequence not found in PDB file:". The file names are correct and I have downloaded the PDB files from PDB. This problem exists for many PDB files. I am enclosing the alignment, top files and error message in log file. I also like to know how to specify the chain ID when working with reference protein with more than one chain.

 

Alignment File
>P1;p00760
sequence:p00760: : : : : : : :
KIVGGYTCGANTVPYQVSLNS--GYHFCGGSLINSQWVVSAAHCYKSG--IQVRLGEDNI
NVVEGNEQFISASKSIVHPSYNS---NTLNNDIMLIKLKSAASLNSRVASISLPTSCASA
GTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDS
CQGDSGGPVVCSGKLQGIVSWGSG-CAQKNKPGVYTKVCNYVSWIKQTIASN-
*
>P1;1fxy
structureX:1fxy: :A : : : : : :
-IVGGYNCKDGEVPWQALLINEENEGFCGGTILSEFYILTAAHCLYQAKRFKVRVGDRNT
EQEEGGEAVHEVEVVIKHNRFTK---ETYDFDIAVLRLKTPITFRMNVAPASLPTAPPAT
GTKCLISGWGNTASSGADYPDELQCLDAPVLSQAKCEASYPGKITSNMFCVGFLEGGKDS
CQGDSGGPVVCNGQLQGVVSWGDG-CAQKNKPGVYTKVYNYVKWIKNTIAANS
*
>P1;1npm
structureX:1npm: :A : : : : : :
-ILEGRECIPHSQPWQAALFQG-ERLICGGVLVGDRWVLTAAHCKKQK--YSVRLGDHSL
QSRDQPEQEIQVAQSIQHPCYNNSNPEDHSHDIMLIRLQNSANLGDKVKPVQLANLCPKV
GQKCIISGWGTVTSPQENFPNTLNCAEVKIYSQNKCERAYPGKITEGMVCAGSSNG-ADT
CQGDSGGPLVCDGMLQGITSWGSDPCGKPEKPGVYTKICRYTTWIKKTMD---
*
TOP file
INCLUDE
SET OUTPUT_CONTROL = 1 1 1 1 1
SET ALNFILE = 'p00760.ali'
SET KNOWNS = '1fxy' '1npm'
SET SEQUENCE = 'p00760'
SET ATOM_FILES_DIRECTORY = '/home/rajesh/alcproj'
SET STARTING_MODEL= 1
SET ENDING_MODEL = 1
CALL ROUTINE = 'model'
Error message
Dynamically allocated memory at amaxseq [B,kB,MB]: 2210071 2158.272 2.108
openf5__224_> Open 11 OLD SEQUENTIAL p00760.ali
openf5__224_> Open 13 OLD SEQUENTIAL 1fxy
openf5__224_> Open 13 OLD SEQUENTIAL 1npm
Dynamically allocated memory at amaxbnd [B,kB,MB]: 5790067 5654.362 5.522
openf5__224_> Open 11 OLD SEQUENTIAL p00760.ali
openf5__224_> Open 13 OLD SEQUENTIAL 1fxy
rdpir___648E> Alignment sequence not found in PDB file: 1 1fxy
recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
 
can someone help
 
Thanks
 
Rajesh R
Research Assistant
Univerisity of Agricultural Sciences
BANGALORE - INDIA


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