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