[phenixbb] SAD Phasing

[Francis E Reyes]

Sena


So is your question related to how autobuild build (or didnt build)  
your chain?
Do the maps support the chain? Perhaps you can just simply build it  
manually to solve your structure?

I've had issues building nucleic acids with phenix.autosol for a  
different reason and rather just build it by hand.




F

On Apr 12, 2010, at 4:13 PM, Rajagopalan, Senapathy wrote:

> Hi,
>
> What I meant was phenix is able to build one of the strands longer  
> than the other strand (but neither of them complete). And whether I  
> ask phenix to build protein or DNA, often times the part of the  
> protein is in the DNA region and vice versa.  The space group is  
> P212121 and no NCS is found.
>
> Thanks
> Sena
>
> On 4/12/10 2:18 PM, "Francis E Reyes" <Francis.Reyes at colorado.edu>  
> wrote:
>
> 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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> Designated as a Magnet hospital for excellence in nursing
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