-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali@salilab.org; Web http://salilab.org

-----Original Message----- From: Bozidar Yerkovich [mailto:bozidar@salilab.org] Sent: Wednesday, February 26, 2003 4:29 PM To: Andrej Sali Subject: modeller problem (fwd)

---------- Forwarded message ---------- Date: Tue, 18 Feb 2003 10:40:55 +0200 From: Liisa laakkonen llaakkon@pcu.helsinki.fi Reply-To: liisa.laakkonen@helsinki.fi To: bozidar@salilab.org Subject: modeller problem

Hello, and good luck in the new place,

I have a heteroatom problem. The system is as follows:

the template (actually 3 but I try first one) the sequence the alignement includes one chain of the template only and the middle part only e.g. structureX:templ:25:A:400:A:undefined:undefined:1.00:1.0

The prosthetic groups are defined as a separate chain, X, and they are observed in the unknown structure, too.

I've included: set hetatm_io = on -----/.., in the alignement BLK residue for fixed unknown structure (+ have ch27 topology files for it)

DON'T KNOW how to mark two chains in the alignment Is it possible? Clearly, the program would like to get the number of residues right, and and complains about the dots in the alignemnt, OR about the missing backbone atoms in the BLK, whichever I edit. The only way I can see possibly working is to edit styronly the pdb files, cut away the C-termini, mark heteroatoms to belong to the subunit A, and change their numbering. I would not like to do this, because I might need the tails later, and eliminating true residue numbers nearly always causes trouble.

Any help would be most welcome.

Sincerely, Liisa Laakkonen University of Helsinki