Dear all,

Finally I solve this problem after I set the stdev as 0.005. I thought that stdev means standard deviation, there might be some other meanings, right? I will check the manual again.

All the best,
Qinghua


-------- Original Message --------
Subject: constraints failed
Date: Mon, 14 Oct 2013 12:19:05 +0200
From: fantasticqhl <fantasticqhl@gmail.com>
To: modeller_usage@salilab.org


Dear all,

I am trying to construct a model with four HIS binding to a copper. I set the distance constraints for ND1--CU as 2.0 angstrom, but the distances between ND1 and CU of the constructed models are around 2.5 angstrom, it seems that the constraints failed. Acctually, when I checked the model, I found that the distances could be around 2.0 angstrom if CU was just moved a little bit.

        rsr.add(forms.gaussian(group=physical.xy_distance,
                               feature=features.distance(at['ND1:13:X'],at['CU:43:Y']),
                               mean=2.00, stdev=0.05))
        rsr.add(forms.gaussian(group=physical.xy_distance,
                              feature=features.distance(at['ND1:14:X'],at['CU:43:Y']),
                               mean=2.00, stdev=0.05))


Could someone tell  me what kinds of reasons could result in restraints failure? Thanks very much!


All the best,
Qinghua