Dear Jeff, Are B-factors taken into account if both orientations don't clash? This is the function of Coot to detect flip. I think it's nice if it is automatically done... already implemented? Thanks, Keitaro 2011/3/2 Jeff Headd :

Hi Maia,

Phenix.refine analyzes Asn, Gln, and His residues at each macrocycle and determines which orientation is likely correct given the local environment of the sidechain. The best orientation will have no steric clashes and satisfy local H-bond donors/acceptors. In cases where there are other model errors in the region of the sidechain and both orientations clash significantly, you'll see the **PLEASE CHECK MANUALLY** warning which indicates that there are likely multiple misfit sidechains that need to be corrected, and refinement alone is not powerful enough to escape the false minimum.

If you want to turn this feature off, you can add main.nqh_flips=False to your refinement call or

main {  nqh_flips=False }

to your param file. However, we highly recommend leaving this option on as it is an excellent diagnostic of model errors.

If you have any further questions please let me know.

Thanks, Jeff

On Tue, Mar 1, 2011 at 5:45 PM, Maia Cherney wrote:

...

Hi,

I am using now the latest phenix version and I am curious how to understand these lines:

Flipped N/Q/H residues before refinement: A  28 HIS A  72 HIS A 141 GLN A 202 GLN A 296 ASN ** A 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN A 388 HIS

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