Well, I guess you can mess with the "overall B-factor correction" in the anneal.inp and rigid.inp files and say, turn them off. NOT a good way to proceed. That is just to let you know where to find it.
If you haven't already done so, do the following after the simulated annealing step. After annealing, run minimization (minimize.inp) and bgroup refinement (bgroup.inp). The grouped B refinement will refine the B factor. Make sure that you keep an eye on how many cycles of refinement you run for each refinement protocol by correlating it with the drop in Rfactor and Rfree. YOu might have to cut back on the no. of refinement cycles in the later stages. Hope that helps. Raji ---------Included Message---------- >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 >_________________________________________________________________ >Don't get caught with egg on your face. Play Chicktionary! >http://club.live.com/chicktionary.aspx?icid=chick_wlmailtextlink > ---------End of Included Message----------
