[phenixbb] MR problem

Randy J. Read rjr27 at cam.ac.uk
Mon Aug 22 00:49:27 PDT 2011


Often in such cases the signal is relatively weak for the second domain, especially at the rotation function step. There are two main things we recommend (which you may have tried). First, lower the threshold for peaks in the rotation search from the default of 75% of maximum to, say, 50%. It may also help to turn off the clustering of rotation peaks. Second, take advantage of anything you might know about the orientation of the second domain. If you have another structure with the same pair of domains their relative orientation is likely to be similar, so you can use a "rotate around" search to restrict the relative orientation within, say, 30 degrees of the first.


Randy Read

Randy J. Read

On 22 Aug 2011, at 08:12, intekhab alam <faisaldbg at gmail.com> wrote:

> Hi there
> I have a data of heterotrimer protein complex  at 2.9A resolution.
> One protein consists of two domains. I tried phaser as well as molrep which gives a solution with only one domain.
> Rotation function and translation function were found to be fine for these solutions.
> I tried to find missing domain of the protein after fixing one of the domain or the other partner proteins using whole part or various truncations of missing domain.
> I also tried to find and build missing domain using Rosetta with the solutions of Molrep or Phaser as template.
> But, there were no solutions, or the solutions are clashed with other domain or proteins.
> Furthermore, R and Rfree is 30 and 40, respectively, and I could not reduce them further.
> There was almost no electron density map in the empty space so that I could not model manually.
> Plz guide me ,how can i look for the missing domain in the protein.
> regards
> -- 
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