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