Jim Pflugrath calls it "molecular substitution" -- I find this a very
neat distinction.
On 19/04/2010 15:50, Ian Tickle wrote:
> I would say it should still be classed as MR: the distinguishing
> feature of MR is surely that it uses an known structure as a starting
> model, not that it does a rotation/translation search. In any case
> the distinction between a rigid-body search and RB refinement is moot.
> At Astex our automated scripts routinely do a limited MR search for
> all our protein-ligand structures, even though it may not be necessary
> in all cases. This is because we have found from experience that RB
> refinement alone is often not sufficient: presumably the degree of
> non-isomorphism induced by soaking and/or freezing the crystals (e.g.
> we often see 5-10% changes in cell parameters) takes it beyond the
> radius of convergence of the refinement. We use a limited search MR
> to avoid issues of finding symmetry-related or origin-shifted
> solutions.
>
> Cheers
>
> -- Ian
>
> On Mon, Apr 19, 2010 at 3:06 PM, Edward A. Berry<[log in to unmask]> wrote:
>
>> Quite a lot of structures in the PDB involve minor variations on structures
>> that have already been solved (different ligands, mutants, high res), so the
>> "solution" involves refining the previous structure against the new data,
>> perhaps starting with rigid body refinement to correct minor variations
>> in cell parameters.
>> Would you include this in "molecular replacement"?
>>
>> Ed
>>
>> Nicholas Keep wrote:
>>
>>> Thanks to several people for helpful comments to my question on the
>>> Proportion of MR in the PDB.
>>>
>>> I got two very detailed responses one from the OCA team at the Weizmann
>>> which went to the Bulletin Board
>>>
>>> "This is what OCA has: From un total of 64,623 PDB structure files,
>>> 30,784 have 'MOLECULAR REPLACEMENT' as Method for Structure Determination.
>>>
>>> However, you must remember that we have a large number of false negatives
>>> Several reasons:
>>>
>>> - Only 47,557 structure files from the total of 64,623 report which
>>> method was used for structure determination. For example, 1CRY whose
>>> title reports using the MR method does not include the info in the
>>> proper REMARK.
>>>
>>> - Users are allowed to write almost anything as the METHOD USED TO
>>> DETERMINE
>>> THE STRUCTURE, making it difficult an accurate report. OCA found PDB
>>> italian
>>> speaking structure files reporting 'MOLECULARE REPLACEMENT' ...
>>> This and other problems are being reported to RCSB."
>>>
>>>
>>>
>>> and one from U of Virginia
>>>
>>> "Based on information from Remark200 lines, 31761 structures were solved
>>> using MR, what comprise for 56.8% of all X-RAY structures (55843).
>>> Considering structures which were determined using 'primitive MR' the
>>> number grows to 34949 (62.6%). There are also some structures determined
>>> using combination of MR with SAD, MAD, SIR and MIR. If we would add them,
>>> the number will increase to 35258 (63.1%)."
>>>
>>> Thanks again
>>> Nick
>>>
>>>
>>>
>>
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