Hi, Michael,

The problem was with the format of the alignment file (you need to say the entries are "structure", not "sequence", if you wish MODELLER to read a structure file), and the second field in the second line of an entry needs to be either the PDB file name or its root (see below). The format of the alignment file is described in the manual ...

Happy modeling, Andrej

>P1;1 structure:1: : : : : : : : : KRAHHNALERRRRDHIKESFTNLREAVP--TLK--GE--KASRAQILKKTTECIQTM* >P1;2 structure:2: : : : : : : : : AREQHNALERRRRDNIKDMYTSLREVVP--DAN--GERVQASRAVILKKAIESIEKG*

-- Andrej Sali, Associate Professor The Rockefeller University, 1230 York Avenue, New York, NY 10021-6399 tel +1 212 327 7550; lab +1 212 327 7206 ; fax +1 212 327 7540 e-mail sali@rockefeller.edu; http://salilab.org

-----Original Message----- From: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org] On Behalf Of Michael Buck Sent: Monday, January 24, 2000 9:06 AM To: modeller_usage@salilab.org Subject: Error using MALIGN3D

MALIGN3D Top files which worked well using Modeler 4 are giving me this error :

fndatmi_284E> Beginning atom index for a residue out of bounds: 0 0 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1

I am using the following script

# MALIGN3D READ_ALIGNMENT FILE = 'pair.aa' SET ATOM_FILES = '1.pdb' '2.pdb' SET FIT_ATOMS = 'CA' MALIGN3D GAP_PENALTIES_3D= 0 2.0, WRITE_FIT = on, WRITE_WHOLE_PDB = off

If anybody has seen this problem, please help.

Thank you Michael Buck

************************************************ Michael Buck NCSU Genetics mjbuck@unity.ncsu.edu Phone (919)515-5759 Fax (919)515-3355 http://www4.ncsu.edu/~mjbuck *************************************************