[phenixbb] Problem avoiding real space refinement

Pavel Afonine pafonine at lbl.gov
Thu Oct 27 14:45:10 PDT 2011


Hi Jerome,

I can't reproduce this myself. I just run it and I can see the output 
like you quote below in both - the log file and terminal screen.
Can you possibly send me the complete reproducer (all inputs and 
commands necessary to reproduce the problem, and explain in details what 
you did to obtain this problem)?

Pavel


On 10/27/11 10:42 AM, Jerome Nwachukwu wrote:
> Interesting. I've also noticed that lines (such as those shown below) 
> are missing from the logfiles whether I 
> select *individual_sites_real_space or not.
>
> |-LOCKIT real space refinement (target=simple): 
> start-------------------------|
> | r_work=0.2098 r_free=0.2283 rmsd bonds=0.004 angles= 1.03           
>         |
> |-----------------------------------------------------------------------------|
>
>
> |-LOCKIT real space refinement (target=simple): 
> end---------------------------|
> | r_work=0.2203 r_free=0.2521 rmsd bonds=0.004 angles= 0.74           
>         |
> |-----------------------------------------------------------------------------|
>
> Could it be that the global *individual_sites_real_space strategy was 
> actually not performed in either case? I would be glad to send you the 
> logfiles off list, if that would be more helpful.
> Thank you,
>
> -Jerome
> Jerome C. Nwachukwu, PhD
> Nettles' Lab
> Dept. of Cancer Biology
> Scripps-FL
> x3297
>
> On Oct 27, 2011, at 1:12 PM, Pavel Afonine wrote:
>
>> 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 <mailto: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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>>
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