Hello all,
I am using modeller 8v1 and trying to build a set of models that all differ from one another. I cannot figure out the equivalent command in 8v1 to the command: 'SET DEVIATION = 4.0 # Amount of randomization between models' in 6v2.
Thank you for your help,
Adam
Adam C. Marko National Resource for Biomedical Supercomputing Pittsburgh Supercomputing Center Pittsburgh, PA 15213 www.psc.edu/~marko
Adam C Marko wrote: > I am using modeller 8v1 and trying to build a set of models that all > differ from one another. I cannot figure out the equivalent command in > 8v1 to the command: > 'SET DEVIATION = 4.0 # Amount of randomization between models' in 6v2.
Just specify 'deviation' when you create an automodel object (see http://salilab.org/modeller/manual/node37.html), e.g. a = automodel(env, alnfile = 'alignment.ali', knowns = '5fd1', sequence = '1fdx', deviation=4.0)
or you can set it after you create the object, e.g. a = automodel(env, alnfile = 'alignment.ali', knowns = '5fd1', sequence = '1fdx') a.deviation = 4.0
Note also that TOP scripts from 6v2 will also work unchanged, provided that the name of the script ends in ".top".
Ben Webb, Modeller Caretaker
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Modeller Caretaker