Re: [modeller_usage] getting pdb's but not fit.pdb's

[Modeller Caretaker <modeller-care@ucsf.edu>]

roac0030 AT flinders.edu.au 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:

from modeller import *
from modeller.automodel import *

env = environ()

a = automodel(env,
              alnfile  = 'mon.ali',     # alignment filename
              knowns   = ('1sto.pdb', '1oro.pdb'), # template codes
              sequence = 'pf_oprt')
a.starting_model= 1
a.ending_model  = 5
a.deviation = 4.0 # Amount of randomization between models
a.library_schedule = autosched.slow # thorough VTF schedule
a.max_var_iterations = 300
a.final_malign3d = True
a.md_level = refine.very_fast
a.make()

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

	Ben Webb, Modeller Caretaker
--
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