[phenixbb] Problem avoiding real space refinement

[Pavel Afonine]

Hi,

yes, this is exactly it. Sorry, I keep promising to clean this 
naming/conception mess one day. Hopefully (thanks Herb), this day is 
approaching fast!

Pavel

On 10/27/11 8:51 AM, Nathaniel Echols wrote:
> On Thu, Oct 27, 2011 at 8:31 AM, Jerome Nwachukwu<JNwachuk at scripps.edu>  wrote:
>> We noticed that in some of our refinements, real space refinement was
>> performed even though we chose not to do this.
>> I tried to opt out of real space refinement as follows:
>> " refine {
>>      strategy = *individual_sites individual_sites_real_space rigid_body \
>>                 *individual_adp group_adp *tls *occupancies group_anomalous
>> ..."
>> however, the R-free is identical whether we select real space refinement or
>> not, and the logfile shows
>> " Validate:
>>                  |--------START--------|  |--------FINAL--------|
>>       residue    map_cc 2mFo-DFc mFo-DFc  map_cc 2mFo-DFc mFo-DFc
>>    "LYS A  18 "  0.9359    16.78    0.00  0.9107    17.60    0.00
>>    "ARG A  19 "  0.9513    21.82    0.00  0.9470    20.97   -6.52<<<
>>    "ARG A  26 "  0.9440    26.72    0.00  0.9474    27.33   -2.43
>>    "ARG A  69 "  0.9685    31.36    0.00  0.9659    32.58    0.00
>>    "GLN A  86 "  0.9681    23.57   -5.81  0.8850    19.29  -18.27<<<
>>    "GLU A  89 "  0.9689    26.30   -4.43  0.8977    23.67  -11.59<<<
>>    "LYS A  93 "  0.9746    25.19    0.00  0.9682    26.47    2.90
>>       ... "
>> and  suggesting that real space refinement was performed.
> That's the rotamer fitting - technically, it's an independent step
> (fix_rotamers=True)  The individual_sites_real_space strategy only
> performs global real-space refinement.
>
> -Nat
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