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------ Forwarded Message From: Michael Grabe mgrabe@itsa.ucsf.edu Date: Mon, 25 Aug 2003 12:33:05 -0700 To: modeller-care@salilab.org Subject: two attached small, pdb files

Dear Modellers,

Let me describe a minor problem I have encountered with modeller 6V2 on Mac OSX,

What I do:

I take a small alpha helix (25 amino acids) and I copy it and translate it.

I then concatenate the two alpha helix pdb files, separating the first and the second alpha helix by a TER line.

Note, the original helix is missing a capping oxygen at the last residue.

Now I renumber the pdb amino acids so that they go from 1 to 50 instead of 1 to 25 and then 1 to 25 (see helices.ini).

I then start to work with this pdb file without any alignment file.

I run this modeller script on the two alpha helices:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% INCLUDE

READ_MODEL FILE = 'helices.ini'

READ_TOPOLOGY FILE = '$(LIB)/top_heav.lib' READ_PARAMETERS FILE = '$(LIB)/par.lib'

GENERATE_TOPOLOGY SEQUENCE = 'temp'

WRITE_MODEL FILE = 'refine0.pdb' OPTIMIZE MAX_ITERATIONS = 100 WRITE_MODEL FILE = 'refine1.pdb' ENERGY %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Now if I look at refine0.pdb generated from modeller, I have a problem.

As I mentioned before amino acids 25 and 50 are missing capping oxygens, but modeller puts them on for me and refine0.pdb has two more atoms than the initial helices.ini.

***Here is the point, the added oxygen to amino acid 25 shifts the labeling of all of the atoms and their positions in the second alpha helix. ***

Look at and compare atoms 201 to 206 in the attached files to see exactly what I mean. Once you see, it will be clear that the optimization that follows has a bit of a tough time since all of the atoms in the second helix have shifted positions.

Any hints about how to make this better?

Thanks, Michael

------------------------------------------------------------------------ -------------------------- Michael Grabe, Ph.D. Post-doctoral Fellow Howard Hughes Medical Institute University of California, San Francisco 533 Parnassus Ave. San Francisco, CA 94143 mgrabe@itsa.ucsf.edu tel: ++ 415.476.6585 http://itsa.ucsf.edu/~mgrabe

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