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

-----Original Message----- From: owner-modeller_usage@salilab.org [mailto:owner-modeller_usage@salilab.org] On Behalf Of Modeller Care Sent: Tuesday, August 19, 2003 8:28 AM To: modeller_usage@salilab.org Cc: tjaart@tuks.co.za Subject: Modelling with metals and hetero

non-member submission forwarded by list-owner ------ Forwarded Message

Date: Tue, 19 Aug 2003 07:27:56 +0200 From: Tjaart de Beer tjaart@tuks.co.za Reply-To: tjaart@tuks.co.za User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.2.1) Gecko/20021204 X-Accept-Language: en-us, en MIME-Version: 1.0 To: modeller_usage@salilab.org 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