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