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RE: malign3D question


Please check the format of the alignment file (there was another recent
similar question). If this does not help, please email us the input top,
alignment, and PDB files.

Thanks, ANdrej

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 ; http://salilab.org

-----Original Message-----
[">mailto:] On Behalf Of Karen
C. Ellis
Sent: Monday, January 21, 2002 11:30 AM
Subject: malign3D question

I was trying to use the malign3D command to do an alignment of three
sequences based on their PDB structures.  I was able to get an inital
alignment from the command malign with no problems.  I used this
alignment as the starting point.  I then copied the commands found on
the user manual page for malign3d (of course changing the file names as
appropriate) to a .top file.  When I look at the .log file I get the
following error

fndatmi_284E> Beginning atom index for a residue out of bounds:  0 0

I have also tried running align3d for two sequences at a time and that
works fine.  Any suggestions on what I am doing wrong?

Karen Ellis