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 xtriage?

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. 

F



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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