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Hi all,
I'm tring to align an amino acid sequence with a
protein (solved by X-ray)
which conteins 6 chains in its PDB
file.
for my job I use the script:
>SET ATOM_FILES_DIRECTORY =
'./../atom_files'
>READ_MODEL FILE = '1icf.pdb' >SEQUENCE_TO_ALI ALIGN_CODES = '1icf', ATOM_FILES = '1icf' >READ_ALIGNMENT FILE = 't.ali', ALIGN_CODES = ALIGN_CODES 't', ADD_SEQUENCE = ON >ALIGN2D >WRITE_ALIGNMENT FILE='t-1fh0.ali', ALIGNMENT_FORMAT='PIR' >WRITE_ALIGNMENT FILE='t-1fh0.pap', ALIGNMENT_FORMAT='PAP but it don't work end the output is:
>iatmcls_286W> MODEL atom not
classified: THR:OT1 THR
>iatmcls_286W> MODEL atom not classified: THR:OT2 THR >iatmcls_286W> MODEL atom not classified: VAL:OT1 VAL >iatmcls_286W> MODEL atom not classified: VAL:OT2 VAL >iatmcls_286W> MODEL atom not classified: THR:OT1 THR >iatmcls_286W> MODEL atom not classified: THR:OT2 THR >iatmcls_286W> MODEL atom not classified: VAL:OT1 VAL >iatmcls_286W> MODEL atom not classified: VAL:OT2 VAL >iatmcls_286W> MODEL atom not classified: SER:OT1 SER >iatmcls_286W> MODEL atom not classified: SER:OT2 SER >iatmcls_286W> MODEL atom not classified: SER:OT1 SER >iatmcls_286W> MODEL atom not classified: SER:OT2 SER >read_al_375E> Unknown residue type,position,sequence: 1 2 >recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 any ideas?
Thanks!
G.
**********************************
Dr. Gianluca Croce
Ph.D. Student DISTA - University Amedeo Avogadro Corso Borsalino 54-15100 Alessandria-Italy Tel_office: +390131287414 Fax: +390131287416 |