is derivative data useful for looking for the missing part of the model?
Hi everyone, I got a partial model, consisting of 80% of the whole molecule, from the molecular replacement. The native data reflects to 2.3 A, and now the R/Rfree= 0.22/0.28. My problem is that the missing part of the model is important for us, but there is not any density for this region now. Meantime, we have several heavy atom derivative data. My question is that if refine the model against the derivative data, will the heavy atom appear in the difference map if existing? Any suggestions on how to use the derivative data to locate the missing part of model? Thanks in advance! Regards, Fengyun
. My question is that if refine the model against the derivative data, will the heavy atom appear in the difference map if existing?
Yes Using the model to find the heavy atom sites and then calculating phases on those sites (without model) might help. ( I believe phenix will output a phase combined map (model + experimental phases)). Multi crystal averaging might help. However, as you come from MR, you should try a prime and switch map on the original data. F On Jun 15, 2010, at 4:59 PM, fn1@rice.edu wrote:
--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
On Tue, Jun 15, 2010 at 4:03 PM, Francis E Reyes
wrote:
Correct, this is the default behavior if you provide a model directly to AutoSol (or Phaser). There is however a semi-automatic way to use the model phases to find sites without biasing the experimental map; see the documentation here: https://www.phenix-online.org/version_docs/1.6.2-432/autosol.htm#anch126 (The AutoBuild step is optional - you could just look at the density-modified map after AutoSol is done.) -Nat
Thanks so much!It looks promising.
If I have two or more derivative data and want to combine all these
information. Can I just do MRSAD individually for each dataset, and
combine them?
引用 Nathaniel Echols
2010/6/15
Short answer: much of this is already automated in AutoSol, and the model phases can be used for methods other than SAD. You'd still run AutoMR to get the model phases, then run AutoSol with all derivatives at once plus model phases. I'm not sure whether it's better to do it as an MIR(AS) experiment, with your native data and the derivatives, or multiple SAD experiments (without native data). Both should be (mostly) straightforward to set up. However, the quality of the final phases still depends on the quality of the derivative data. If you already have decent phases it is often very easy to find heavy atoms by eye in the anomalous (or isomorphous, I guess) difference maps, but this doesn't always mean that you can calculate good phases using those sites. It might be a good idea to try running Xtriage on each of the derivative datasets first to assess the anomalous signal. -Nat
participants (3)
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fn1＠rice.edu -
Francis E Reyes -
Nathaniel Echols