[sharp-discuss] phase extension

Clemens Vonrhein vonrhein at globalphasing.com
Mon Aug 14 08:46:03 BST 2006


Dear Nick,

usually I would always use autoSHARP with all reflections, since it
tries to automatically decide what a good resolution cut-off for the
HA-detection is. However, especially in SAD the analysis for deciding
on this resolution cut-off can be a bit unreliably. The it is
recommended to start with a lower resolution.

Once you've found some HA sites (in autoSHARP or outside ... doesn't
matter), I recommend the following:

  1. create a file with extension .hatom in your sharpfiles/datafiles
     directory

  2. edit it to hold the fractional coordinates of your HA sites (the
     ones you trust), e.g.

     ATOM Se 0.1234 0.2345 0.3456
     ATOM Se 0.4567 0.5678 0.6789

  3. start autoSHARP using the full resolution range

  4. there should be a pull-down menu, where you now can select your
     newly created *.hatom file

  5. make sure to tell autoSHARP the maximum number of Se-atoms you
     expect per monomer! autoSHARP will try and complement the found
     HA sites, since you might not have found all of your Se sites.

Hope that helps ...

Cheers

Clemens


On Sat, Aug 12, 2006 at 04:19:04PM -0400, Noinaj wrote:
> Hi, 
> 
> I have found Se sites using autoSharp with resolution limits 30-6.0 angstroms (as suggested by NOTES within autoSHARP).  Yet my actual dataset (as well as native dataset) is up to 2.4 angstroms.  What is the best approach to do phase extension to higher resolution cutoff within SHARP/autoSHARP?  
> 
> Could I use the initial sites that I find from ha search and then refine and phase using highest resolution cutoff of 2.4? 
> 
> Thanks for all your advice in advance!
> 
> 
> 
> Cheers,
> Nick
> 
> 
> 
> 
> ________________________________________
> 
> Nicholas Noinaj
> University of Kentucky School of Medicine
> Department of Molecular and Cellular Biochemistry
> Biomedical Biological Sciences Research Building, Rm 236
> 741 S. Limestone
> Lexington, Ky 40536
> Lab:  859-323-8183
> Home:  859-228-0978
> noinaj at uky.edu
> www.noinaj.com
> 

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