Dear Modeller
I was using the script Align2D.top below to run modeller with version 6.2. Now that we installed version 7, I just can't get it to work. I get the following message:
read_al_375E> Unknown residue type,position,sequence: 1 2 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
Could you please let me know what is wrong? Thanks, Paula Kuser
Align2D.top
############################################# # ALIGNING OUR TARGET WITH THE TEMPLATE # # file.pdb - your template pdb file # pdb name - template code # seq.txt - target file in pir format # seq - target code # file.ali - constructed alignment file ############################################# # Include MODELLER library scripts #INCLUDE # Defining our local pdb directory for input #SET ATOM_FILES_DIRECTORY = '/db/pdb' # Reading template pdb file READ_MODEL FILE = '1ig8.pdb' # Defining code of the template SEQUENCE_TO_ALI ALIGN_CODES = '1ig8' # Reading our target READ_ALIGNMENT FILE = 'seq.txt', ALIGN_CODES = ALIGN_CODES 'HEX', ADD_SEQUENCE = on # Alignment ALIGN2D # Alignment in pir formate WRITE_ALIGNMENT FILE='HEXTC.ali', ALIGNMENT_FORMAT = 'PIR'
Here is the seq.txt file:
######################################################### # #TARGET SEQUECE IN PIR FORMAT # ########################################### >P1;HEX sequence:HEX:.:.:.:. MSARLNNLLQHIAVKDKDSDTMRHLKQRMALASLANQFTVGKDHLKQLMLYMVHQMIEG LEGRESTLRMLPSYVYKTDPSKATGVFYALDLGGTNFRVLRVTCKEGRVADRVDAKFVI PQQALQGTAEDLFGFIAQSVKKMMEQKAPEDLNRTVPLGFTFSFPTEQKGVDHGFLIKW TKGFSTRGVEGKDVVELLQKALKRMEVKVKVVALCNDTVGTLITNYFFDPDTQVGVIIG TGSNACYFEDAYAVTKEPSVAARGTTQTPINMECGNFDSKYKFVLPVTAYDEAMDAVTP NRNFQTQEKMVSGMYLGEISRRMIAHLAELHCLPSALASKMAKPWSFETKFMGMISADR MPGLQFTRQVFQELFQVDVTDVADLHVIRDVCCLVRGRAAQISAMFCSAPLVKTRKEGR ATVAIDGSVFEKTPSFRRLLQQNMNAILGPGCDVTTALARDGSGIGAAFISALVVNDK*
Paula Kuser Falcão Laboratório de Bioinformática Estrutural Embrapa Informática Agropecuária