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----- Forwarded message from Sherin Yang sherin@sina.com -----

From: "Sherin Yang" sherin@sina.com To: modeller-care@salilab.org Subject: can't write the model structure Date: Sat, 6 Sep 2003 02:17:46 +0800 X-Mailer: Microsoft Outlook Express 6.00.2800.1106

Hi, all

I have write a TOP script and want to align a sequence with a structure using ALIGN2D. but I can't get the proper alignment result. The structure's sequence isn't contained in the alignment file. And the log file didn't inform any error information. The following is the TOP scrip, and the attachment is the PDB file.

The 1CF8 contains two chains, L and H. Maybe there is something wrong in "MODEL_SEGMENT='1:L' 'X:L' "?

######################################################## READ_MODEL FILE = '1CF8.pdb', MODEL_SEGMENT='1:L' 'X:L'

SEQUENCE_TO_ALI ALIGN_CODES = '1CF8L'

READ_ALIGNMENT FILE = query_mod.ali', ALIGN_CODES = 'query'

ALIGN2D

WRITE_ALIGNMENT FILE = 'align2d.ali', ALIGNMENT_FORMAT = 'PIR' ###########################################################

Thank you !

Sherin

----- End forwarded message -----