Hi everyone,
I have some basic questions about CNS. First, I am wondering if there is
anywhere I can set my initial B-factor during my early refinement. When I
generate my initial model in generate.inp, I can set the B-factore. However,
after I did the rigid.inp and anneal.inp, the B-factor just go up to more than
100 by itself. I look through the input files, and couldn't find where to set
the B-factor. Do I have to set the B-factor by hand each time? Or will the
crazy B-factor affect my refinement? Second, I am refining a new protein/DNA
complex. I started with the DNA alone. After rigid body refinement I got ~1%
decrease of Rf. But when I tried anneal after that, the Rf just went up much
higher than where I started? If you work on a protein/DNA complex, what is your
stategy? Will the anneal help refine the DNA alone? How much decrease of Rf
usually you can get from refining just DNA? Third, I was wondering if I want to
extend my resolution, do I have to make sure my cv file was made with the
highest resolution? Thank you for your suggestion!
Cortney
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