[phenixbb] SAD Phasing

Francis E Reyes Francis.Reyes at Colorado.EDU
Mon Apr 12 12:18:13 PDT 2010

The strangest part of your request is that you can fit one side of a  
double helix. You expect the complementary side (W-C pair) right?

What's the space group? Is it one of the cursed space groups? http://www.ccp4.ac.uk/dist/html/twinning.html#likely_operators
What are the moments of intensities of your dataset as reported by  

Did the self rotations indicate NCS to relate the dimer in your  
asymmetric unit? How much of the asu can you build currently? If a  
lot, does a 2fo-fc map with your model indicate the other  
complementary strand?

In my experience,  removal of heavy atom sites won't account for a  
particular feature of your electron density missing, it'll deteriorate  
the entire map indiscriminately.


On Apr 12, 2010, at 3:08 PM, Rajagopalan, Senapathy wrote:

> Hi Everyone,
> I have been trying to solve a structure of a protein-DNA complex  
> using SAD data, but am running into problems and have some questions  
> on how phenix solves it. From Mathews coefficient calculation, I  
> know that my protein binds to the DNA as a dimer in the asymmetric  
> unit. And when I use this information to specify the the number of  
> heavy atoms to look for, I always get more (1.5-2X, depending on  
> what resolution cutoff I use) in the final heavy atom sites pdb  
> file. More importantly, the map looks ‘incomplete’ in the sense that  
> part of one of the strands in the double stranded DNA is missing. My  
> question is if this is the result of phenix using some incorrect  
> sites (such as with low occupancy) while phasing. If so, then how  
> can I fix it. I have tried deleting the low occupancy sites and  
> reading the edited heavy atom sites file explicitly using  
> sites_file=ha.pdb, but it doesn’t seem to help.
> Also, if I just use solve to find the heavy atom sites, those tend  
> to be different too... Any suggestions here would be appreciated.
> Thanks
> Sena
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