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Re: [modeller_usage] User defined restraints

Dimitry.A.Suplatov wrote:

I use the following script
---------------------------------------------------------------------------------------------
...
class mymodel(automodel):
    def special_restraints(self, aln):
        rsr = self.restraints
        for ids in (('OD1:282:B', 'CA:765:B'),
                    ('OD2:282:B', 'CA:765:B'),
                    ('OD1:285:B','CA:765:B'),
                    ('OD2:460:B', 'CA:765:B'),
                    ('OE2:152:A', 'CA:765:B')):
            atoms = [self.atoms[i] for i in ids]
            rsr.add(forms.upper_bound(group=physical.upper_distance,
                                      feature=features.distance(*atoms),
                                      mean=2.5, stdev=0.1))
def special_restraints(self, aln): 
        rsr2 = self.restraints
        for ids1 in (('OE2:152:A', 'CA:765:B')):
            atoms = [self.atoms[j] for j in ids1]
            rsr2.add(forms.upper_bound(group=physical.upper_distance,
                                      feature=features.distance(*atoms),
                                      mean=2.3, stdev=0.1))
You can't define the same routine twice and expect both of them to work! Only the second one will get called - the first will be ignored. Just combine the two routines into one. 


Then I get this error
_modeller.error: indxatm_278E> No ":" in ATOM:RESID[:CHAINID] atom identifier: O
I am using python for the first time so that must be some problem with the script. 

Yes, it's because of the way Python handles tuples. In your script you have:

         for ids1 in (('OE2:152:A', 'CA:765:B')):
             atoms = [self.atoms[j] for j in ids1]
i.e. your intention is to go through a list of pairs (just one pair in this case) and for each one assign 'atoms' to be a pair of atom objects. But in Python you can't define a one-element list that way - Python just ignores the second pair of parentheses. Instead, you need to do: 

         for ids1 in (('OE2:152:A', 'CA:765:B'),):
             atoms = [self.atoms[j] for j in ids1]
i.e. add a trailing comma. See http://docs.python.org/tut/node7.html#SECTION007300000000000000000 

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
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