The cooot method is easiest, as long as you have model coordinates. Then
coot works out the transformation between molecule 1, 2, etc and
averages any map requested to cover molecule 1.
However if you dont have a model it is very tricky to get a proper
transformation matrix.
If you have enough heavy/anomalous sites programs like profess will try
to suggest transformation relating one subset to another.
If you have some phases then buccaneer will try to build a model and
look for any acceptable NCS transformation.
Once you have the transformations mapaverage will work..
Eleanor
On 09/22/2011 05:10 AM, Jens Kaiser wrote:
> Hui/Phoenix,
> It is pretty hard to say from what you describe which method is right.
> The NCS maps in coot will give you a correct - but not as good of an
> estimate of your density - if, and only if, you have enough of a model
> and you have defined your NCS master and "slave" chains correctly. If
> you have chemically different but similar subunits and you don't check
> them correctly in the NCS ghosts dialog, you'll get bad results.
> CCP4 map average (from the map and mask utilities) is pretty tricky,
> most of the times;
> When I had to do averaging of anomalous difference maps, I found it
> most useful to do cyclic averaging of your "normal" (i.e. non-anomalous)
> map, either with dm, ave/rave or MAIN (and probably phenix, though I
> have not tried it); that will give you good indications of the quality
> and validity of your averaging (i.e. backtransformation R factors;
> correlation coefficients tend to be also more reliable). Then use these
> phases (rotated, but the ccp4i fft task will do that for you if you
> select "anomalous map") to calculate your "averaged anomalous map" with
> your DANOs and the averaged phases.
> This seems to me the most robust and reliable method of averaging
> anomalous maps in the general case. If you have your NCS related
> molecules defined properly, you might want to add coot's average maps on
> top of that, but it is unlikely to improve the outcome.
>
> Cheers,
>
> Jens
>
>
> On Wed, 2011-09-21 at 16:45 -0700, Hui Wang wrote:
>> Dear all,
>>
>> I am wondering if anybody did NCS average for Anomalous map. Based on
>> my knowledge, there are two days to do it.
>>
>> 1, Use Map average in CCP4 program (input from map which cover unit
>> cell, create averaged density for whole unite cell )
>> 2, Use NCS map in coot program.
>>
>> However, I got different results from both ways. I am not sure which
>> one is corret. Someone can help me with that?
>>
>>
>> Thanks a lot
>>
>> Phoenix
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