[phenixbb] Does PHENIX exclude Rfree reflections in maps?

[Thomas C. Terwilliger]

Hi Pavel and Joe,

I carried out a test to see if (1) excluding a super-free set completely
from automated structure solution affects the results and (2) if the
super-free R that results is different from the standard free R obtained
with all data and excluding the free set only from refinement.

Here are the results:

A = structure

B, C and D are for the run with a super-free set excluded from all
calculations.  B and C are work and free R for the reflections included in
the calculation. D is the R for the super-free set.

E and F are work and free R for the same datasets, run in the same way,
but without any super-free set.

   A                  B       C         D                      E         F
                   ---super-free-run----      --standard run--
 structure        work free  super-free     work  free
 1029B           0.31 0.38   0.41          0.29    0.36
 1038B           0.22 0.26   0.26          0.24    0.28
 1071B           0.28 0.33   0.35          0.26    0.30
 rab3a-sad       0.31 0.35   0.38          0.29    0.34
 rnase-p         0.28 0.32   0.31          0.28    0.29
 calmodulin      0.26 0.27   0.27          0.27    0.29
 cobd-sad        0.24 0.26   0.26          0.24    0.28
 insulin         0.27 0.30   0.29          0.25    0.26
 nsf-n           0.23 0.26   0.26          0.21    0.24
 ut-synthase     0.24 0.29   0.28          0.24    0.28

 mean            0.26 0.30   0.31          0.26    0.29

Conclusions:
(1) super-free is very nearly the same as free in the matched set.
(2) leaving out super-free data does not make a lot of difference in these
actual cases. (Perhaps it might in worse data sets)
(3) so it would be ok to take out super-free set, but it is not necessary.

All the best,
Tom T



>> Hi Pavel and Joe,
>>
>> I'm glad you put that option in, Pavel.  However for model-building it is
>> not so straightforward. Normally we are building into density-modified
>> maps. Density modification works poorly when a significant set of
>> reflections is excluded, so this becomes impractical. We could exclude
>> those reflections in the map only, but they will have been used in density
>> modification so they are no longer truly free.  I don't have a good
>> solution for that.
>>
>> I am guessing that for model-building, the free R is hardly affected,
>> compared to refinement against the map, though I haven't tested this.
>>
>> All the best,
>> Tom T
>>
>>>> Hi Joe, hi Tom,
>>>>
>>>> until recently, all reflections (work and test) were used in map
>>>> calculation. When I added a real-space refinement option to
>>>> phenix.refine I spent a day thinking hard about why Rfree was almost
>>>> always equal to Rwork after real-space refinement, until I realized
>>>> that
>>>> I have to exclude test reflections from map calculation, and that fixed
>>>> the problem.
>>>>
>>>> I think it depends on the task:
>>>>
>>>> - for things like real-space refinement (where the map is heavily used)
>>>> or automated model building, the test reflections have to be excluded
>>>> from map calculation;
>>>>
>>>> - for catching a tiny detail (looking at weak ligand density = slight
>>>> map use) or fixing a few side chains, all reflections should be used,
>>>> since 10% of data put aside may sometime significantly affect map
>>>> quality.
>>>>
>>>> Pavel.
>>>>
>>>>
>>>> On 9/30/09 11:51 AM, Tom Terwilliger wrote:
>>>>> Hi Joe,
>>>>> In PHENIX R-free reflections are included in your maps.
>>>>> All the best,
>>>>> Tom T
>>>>>
>>>>> On Sep 30, 2009, at 12:47 PM, Joe Krahn wrote:
>>>>>
>>>>>> Does PHENIX exclude R-free reflections when computing maps? IMHO, it
>>>>>> is
>>>>>> bad to use test reflections in maps, or anywhere else other than
>>>>>> computing R-free, but opinions vary. If some people still want test
>>>>>> reflections in maps, maybe it could be an option.
>>>>>>
>>>>>> Thanks,
>>>>>> Joe Krahn
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>>>>
>>
>>