The "." is a place holder "residue" in modeller. It takes care of any
residue type that is not defined in the library. You should add this at the
end of alignment, after a chain break "/" and run modeller. The waters are
represented as "w".
---
Eswar Narayanan, Ph.D
Mission Bay Genentech Hall
600 16th Street, Suite N474Q
University of California, San Francisco
San Francisco, CA 94143-2240 (CA 94107 for courier)
Tel +1 (415) 514-4233; Fax +1 (415) 514-4231
http://www.salilab.org/~eashwar
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Subject: Modelling with metals and hetero
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Date: Tue, 19 Aug 2003 07:27:56 +0200
From: Tjaart de Beer <>
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Subject: Modelling with metals and hetero
I have followed the method in the Modeller
manual on how to model with water and metals or hetero atoms. The
template includes a ligand, metal atom and water molecules. I would like
to know how to incorporate this into the newly built model. So far I
have succeeded in adding waters during modelling but the metal atom and
the ligand is still not in the model. Any help would be greatly appreciated.
Thanks!!
Tjaart
--
Tjaart de Beer
Department Biochemistry
Agricultural Building
Faculty of Natural Sciences
University of Pretoria
Lynwood rd
Pretoria
South Africa
0001
Tel: +27 12 420 2990
Cell: +27 83 504 7914
Fax: +27 12 362 5302
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