[phenixbb] Fwd: Alternative method to Phenix_mr_rosetta

Pavel Afonine pafonine at lbl.gov
Thu Feb 18 19:02:45 PST 2016

Hi Henry,

sounds exciting! Why not just go to PDB database and select test cases 
you want? There are about 116085 entries as of today, which makes it a 
rich resource! There are plenty with high and super-high solvent content 
- I surveyed for this some time not too long ago. What's good is that 
you have the answer - the published model that you can always use to 
compare with!

Wrestling with unsolved structures may be tricky because they may be 
unsolved not because of the phase problem but something else, such as 
various data & crystal pathologies.

Good luck!

On 2/18/16 18:53, Henry Fang wrote:
> Hi All,
> Our group is working on an ab initial density modification method to 
> solve the phase problem.
> Last year, I applied the methods to the cases with a initial template 
> which has already been correctly placed in the unit cell.
> I tried several cases in the Terwilliger, T. C., et al. (2012). 
> "phenix.mr_rosetta: molecular replacement and model rebuilding with 
> Phenix and Rosetta". Starting from the templates provided in 
> thehttp://www.phenix-online.org/phenix_data/terwilliger/rosetta_2011/I 
> can get a initial density map, then apply our method to reduce the 
> phase difference to around 50° in the highest experiment data resolution.
> Now, I might want to try more blind cases with our methods. If we can 
> solve more structures, that would be more convincing.
> Do you have some suggestions? Where could I find some more unsolved 
> structures? I might need structures with placed template and high 
> solvent content (at least above 50%).
> Thanks,
> Henry

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