Hi, I'd like to refine two segments of the model I built by the loop refinement procedure, according to FAQ3 in the manual (version 4) the top file I used was:

INCLUDE

SET SEQUENCE = 'BRB2' SET MODEL = 'BRB2.ini' #initial model SET ATOM_FILES_DIRECTORY = './' SET STARTING_MODEL = 1 SET ENDING_MODEL = 50

SET MD_LEVEL = 'refine1' SET RAND_SEED = -34871

CALL ROUTINE = 'loop'

#cluster the models CALL ROUTINE = 'cluster', ID1 = STARTING_MODEL, ID2 = ENDING_MODEL

SUBROUTINE ROUTINE = 'select_atoms' PICK_ATOMS SELECTION_SEGMENT = '66:' '72:', SELECTION_STATUS = 'initialize' PICK_ATOMS SELECTION_SEGMENT = '242:' '258:', SELECTION_STATUS = 'add'

RETURN END_SUBROUTINE -----------------------

I got the following message in the log file:

TRANSFER RESIDUE NUMBERS AND CHAIN ID FROM MODEL2 TO MODEL: (ALIGNMENT = model2(1st in aln), model(2nd in aln))

# ALGNMT CODE ATOM FILE

1 BRB2 2 BRB2

END OF TRANSFER OF RESIDUE NUMBERS

errdih__E> SIZE1*SIZE2 = 0 1 33 LYS errdih__E> SIZE1*SIZE2 = 0 1 34 SER errdih__E> SIZE1*SIZE2 = 0 1 35 SER errdih__E> SIZE1*SIZE2 = 0 1 36 CYS errdih__E> SIZE1*SIZE2 = 0 1 67 ASN

can you explain what this message mean and how is important for the final models? thanks a lot, Paola

-- dott. Paola D'Alessio Universita' degli Studi di Salerno Dipartimento Scienze Farmaceutiche via Ponte Don Melillo, 84084 Fisciano (Sa), Italy tel.+39 089 962822; e-mail: pdalessio@unisa.it