[phenixbb] advice for refinement with anomalous information

[vincent Chaptal]

Hi,

the refinement of my structure brings me to a new point where I would
appreciate any input.
- I solved the structure by molecular replacement.
- The refinement looked good, I was almost ready to deposit but there
always was a fairly big blob of density that i couldn't explain, loosely
coordinated to the protein and far from the active site.

To try to identify what it could be, i calculated an anomalous
difference map (data collected at 1A) and I see a peak right in the
middle of this density.
I have BaCl2 in my crystallization solution so it is the likely guilty
ion! (and with further look, it looks like a loose metal site)

So now, I want to refine with Barium in the density and I was wondering
what was the best way to do it, and since there is anomalous signal, why
not use it?
* I updated to the new version of phenix and it reads I+ and I- (while
the previous version didn't) but under the refinement settings, the
target function ML-SAD is still for developers only. Is it a good idea
to use the anomalous Is for refinement, or:
* should I re-run Phaser-EP to have phases to use in phenix.refine, or:
* should I not bother, the signal is weak anyway (1 barium/ ~400
residues) and continue with my non-anomalous scaled dataset and use the
anomalous signal only for a figure to explain why I put the metal here.

(resolution of 3.4A, quite anisotropic)

I can also try everything but I'd like to understand what would be best.
Thanks very much for your help
vincent



--

Vincent Chaptal

Dept. of Physiology at UCLA

http://www.physiology.ucla.edu/Labs/Abramson/index.html
<http://www.physiology.ucla.edu/Labs/Abramson/index.html/>

Phone: 1-310-206-1399


IMPORTANT WARNING:  This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential.  You, the recipient, are obligated to maintain it in a safe, secure and confidential manner.  Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.