Hi Li-Zhi Mi, - make sure that the restraints are actually used: look ".geo" file - it contains a list of all geometry restraints used in refinement; - changing the wxc_scale will not necessarily help (although it might) since it is a global weight used for the whole target; - try idealizing the geometry of this problem fragment before refinement; - you can also edit the corresponding CIF file to decrease the sigmas for these particular restraints. Pavel. On 1/22/2009 7:06 AM, Li-Zhi Mi wrote:
Hi, I am using phenix to refine a low resolution structure. The problem I had is that the geometry of disulfide and NAG in the refined structure is not right. I did use a very tight geometry restrains. Both wxc_scale and wxu_scale are set to 0.05. In the refined structures, the sulfur of one cys is very close to the Cb of its disulfide partner. For NAG part, C2-N2-C7-O7-C8 should be in the same plane. But they are not. Is there a way to adjust these violations? Thanks in advance for the helps, Li-Zhi Mi,
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