Re: [modeller_usage] getting pdb's but not fit.pdb's
To:
Subject: Re: [modeller_usage] getting pdb's but not fit.pdb's
From: Modeller Caretaker <>
Date: Wed, 09 May 2007 09:25:03 -0700
Cc:
wrote:
hey, i'm new to modeller. I can use modeller and and get homology models of
proteins but when it comes to writing the superposed pdb's (the x_fit.pdb's) it
comes up with an error and doesn't...
i've included the .top, .ali, and .pdb as well as a screenie of the error. any
help would be greatly appreciated.
TOP scripts have been deprecated for a long time now, so you will not be
able to use them for anything other than basic comparative modeling, as
you've seen. The solution is to use the equivalent Python script
instead, which would look something like:
If for some reason you are particularly attached to TOP, you can fix the
bug that's affecting you by applying the 'top-commands.patch' file, in
the wiki at http://salilab.org/modeller/wiki/Patches