Assuming that the MR solution is correct (I agree with Eleanor, that you
need to be certain about your selection of space group), then use your
complete model of chain A superimposed on chains B, C, and D. Then refine
and build the heck out of it. In a similar situation, it was relatively
easy for me to find two out of three molecules by MR. We were never really
convinced that there was a third (Matthews coefficient dicey, suggesting
either 2 or 3). After substantial refinement and building, the third chain
was apparent, and we rebuilt it completely. Looking at the average
B-factors of each chain, and the overall packing environment, chain A was
tight, chain B looser, and chain C will substantially fewer contacts.
Bernie Santarsiero
On Tue, February 13, 2007 10:07 am, Eleanor Dodson wrote:
> Sometimes this sort of disorder is due to an error , so the first thing
> is to check very carefully that the solution makes sense.
>
> Why are you so sure there are 6 copies in the asymmetric unit?
>
> In situations like this I first worry about SG.
>
> Is there a pseudo-translation vector? This can make it hard to decide on
> the SG..
>
> Is there an alternate spacegroup with fewer molecules in the asymm unit?
>
> What does the self rotation show?
>
>
>
> Yanming Zhang wrote:
>> Dear All,
>>
>> Maybe this is a trivial question:
>>
>> My data should have 6 molecules in one assymetric unit. MR could find
>> out 4 molecules. After this, no matter how hard I have tried, no more
>> molecules can be found. At this stage, I suppose that all other copies
>> are dis-ordered. And go ahead to do refinement with 4 molecules (ABCD)
>> available.
>> The density for A is quite good. But for BCD are very dis-ordered.
>> Many breaks in chains. I'd like to ask you:
>> In a situation like this, should I:
>> A, Use NCS for all copies?
>> B Do not use NCS at all?
>> C, Use NCS just for BCD? (even dis-ordered, but similar)?
>> What is the trick to lower down Rfree as soon as possible, if you have
>> experienced the same situation before?
>>
>>
>> Thanks
>>
>> Yanming
>>
>>
>
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