i ran your sample file for id_table modified for a group of 89 sequences. i used the HUGE binary. It appears DENDROGRAM failed. The program printed out all files, except the dendrogram did not appear in the log file. The program never terminated running after 45 minutes, i killed it. all other files were written within about 5 minutes. i send separately the full log file. i append here the top of the log file and the top file. i send separately the alignment file if you want (please do not make it public). Tim

# Example for: ID_TABLE, SEQUENCE_COMPARISON, PRINCIPAL_COMPONENTS, DENDROGRAM

# Pairwise sequence identity between sequences in the alignment.

# Read all entries in this alignment: READ_ALIGNMENT FILE = 'ywtd89.ali'

# Calculate pairwise sequence identities: ID_TABLE MATRIX_FILE = 'ywtd89_id.mat'

# Calculate pairwise sequence similarities: SET RR_FILE = '$(LIB)/as1.sim.mat', MAX_GAPS_MATCH = 1 SEQUENCE_COMPARISON MATRIX_FILE = 'ywtd89.mat', VARIABILITY_FILE = 'ywtd89.var'

# Do principal components clustering using sequence similarities: PRINCIPAL_COMPONENTS MATRIX_FILE = 'ywtd89.mat', FILE = 'ywtd89.princ'

# Dendrogram in the log file: DENDROGRAM _______________________________________________________________________

MODELLER 4h, June 16, 1997

PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS

v Copyright(c) 1989-1997 Andrej Sali All Rights Reserved

v Written by A. Sali, R. Sanchez & A. Badretdinov Rockefeller University, New York, USA Harvard University, Cambridge, USA Imperial Cancer Research Fund, London, UK Birkbeck College, University of London, London, UK

Array dimensions (!8/9/96!):

Maximum number of residues : 1000 Maximum number of atoms : 16000 Maximum length of alignment : 1000 Maximum number of sequences in alignment : 101 Maximum number of restrained features : 160000 Maximum number of restraint parameters : 1600000 Maximum number of restraint atoms : 480000 Maximum number of non-bonded atom pairs : 90000 Maximum number of non-bonded restraint types : 1 Maximum number of non-bonded restraint type parms: 1 Maximum number of explicitly excluded pairs : 100 Maximum number of pseudo atoms : 200 Maximum optimization schedule length : 50

MODELLER is compiled in : single precision Job starting time : 05-Apr-98 11:39:55