It could be that your partial model has a loop, not present in the true solution, that is causing a clash. You could run Phaser again with the anti-bumping restraint weakened or disabled, or more carefully edit your partial model.
Dale Tronrud On 3/10/2012 11:33 PM, xiaoyazi2008 wrote:
Hi All, I have an interesting thing to share. 2.3A dataset with good quality, P21 Partial model is available (~60% of the target protein). It seems that there are 4 copies in the ASU (Matthews_coef 2.6, 53%solvent) Molecular replacement gave two copies of the model (Z scores are R6.2, T6.2, R6.8, T13.4). The solution is very clear. It could not locate the rest two copies. However, a quick refmac5 refinement gave a very high R factor. The funny part is the symmetry operation in Coot. As shown in the JPEG figure, it looks like there should be another two copies (based on strong fo-fc green map), which locate in the empty space between models found by Phaser. Why is that Phaser could not find the remaining two copies even there are strong fo-fc density? Any suggestions... Thanks a lot! Zhihong
