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<P>What does it say in the log?<BR><BR></P></DIV>
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<DIV></DIV>From: <I>"" <jinlian05@lzu.cn></I><BR>Reply-To: <I>jinlian05@lzu.cn</I><BR>To: <I>modeller_usage@salilab.org</I><BR>Subject: <I>[modeller_usage] using model-loop-refine in Modeller9v1</I><BR>Date: <I>Tue, 17 Apr 2007 16:49:01 +0800</I><BR>>Hi,<BR>>I am new to modeller and I have trouble creating a homology model of a<BR>>protein using model-loop-refine. I modified the model-loop-refine.py script as<BR>>shown below and I got error messages. I would appreciate it if any one<BR>>can give me any suggestion.<BR>>Thanks.<BR>><BR>>from modeller import *<BR>>from modeller.automodel import *<BR>><BR>>log.verbose()<BR>>env = environ()<BR>><BR>>env.io.atom_files_directory = './:../atom_files'<BR>><BR>># Create a new class based on 'loopmodel' so that we can redefine<BR>>#
select_loop_atoms<BR>>class myloop(loopmodel):<BR>> # This routine picks the residues to be refined by loop modeling<BR>> def select_loop_atoms(self):<BR>> return selection(self.residue_range('53:', '67:')<BR>> (self.residue_range('89:', '96:')<BR>> (self.residue_range('118:', '144:')<BR>> (self.residue_range('166:',
'177:')<BR>> (self.residue_range('199:', '221:')<BR>> (self.residue_range('243:', '254:'))<BR>><BR>>a = myloop(env,<BR>> alnfile = 'seg.ali', # alignment filename<BR>> knowns = '1u19A', # codes of the templates<BR>> sequence =
'mrg1', # code of the target<BR>> loop_assess_methods=assess.DOPE) # assess each loop with DOPE<BR>>a.starting_model= 1 # index of the first model<BR>>a.ending_model = 1 # index of the last model<BR>><BR>>a.loop.starting_model = 1 # First loop model<BR>>a.loop.ending_model = 2 # Last loop
model<BR>><BR>>a.make() # do modeling and loop refinement<BR>><BR>>This is the error:<BR>> File "model-loop-refine.py", line 21<BR>> m = myloop(env,<BR>> ^<BR>>SyntaxError: invalid syntax<BR>><BR>><BR>><BR>>_______________________________________________<BR>>modeller_usage mailing list<BR>>modeller_usage@salilab.org<BR>>https://salilab.org/mailman/listinfo/modeller_usage<BR></FONT></BLOCKQUOTE></div><br clear=all><hr>Txt a lot? Get <a href="http://g.msn.com/8HMAENUK/2755??PS=47575" target="_top">Messenger FREE on your mobile.</a> </html>