[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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