Forwarded to modeller_usage from the listowner.

------ Forwarded Message From: Liisa laakkonen llaakkon@pcu.helsinki.fi Reply-To: liisa.laakkonen@helsinki.fi Date: Wed, 26 Feb 2003 12:30:50 +0200 To: modeller-care@salilab.org Subject: heteroatoms & loop_select

Dear Modeller-Man,

A question about loops.

I cannot get the atom selection for loops to work. I SET DO_LOOPS = 1

and then select_loops as in example 3. Whatever numbers I put in for the loops (from the beginning of the chain, or from the middle), the whole protein is "initialized" to a neat straight polypeptide chain. Any suggestions?

I also include a question from two weeks ago, for the case it was lost during your move.

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

the template (actually 3 but 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 studied: 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 inthe alignemnt, OR about the missing backbone atoms in the BLK, whichever I edit. The only way I can see possibly working is to edit stronly 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 liisa.laakkonen@helsinki.fi

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