I havent a reference for the "correct" value of the CC - it is just
based on maps I have seen solved then checked out later.
but if your final model gives a very poor CC with a map calculated from
experimental phases, either for parts of the structure, or for the
whole, it is time to worry. Maybe your phases are bad - poor
measurements, low solvent content, incorrect heavy atom sites, etc.
Or maybe your model has some serious errors?
But of course all crystal structures have some parts better ordered than
others and for those bits the exptlly phased map may have weak density,
espec. after solvent flattening.
eleanor
[log in to unmask] wrote:
> Hi Eleanor:
>
> Do you have some references in mind that discussed the value of CC (say
>> 0.5) to be able to build the structure? Didn't find one for right now:-(
>
> By the way, probably a "weak" question, In the case "a lousy model will
> give poor CCs even if the map is brilliant", we still accept this model
> dispite the poor CC, right? Sorry that I didn't get practically involved
> too much in real model building, but I just heard that model is more
> frequently built manually by eyes, not CC etc.
>
> Best Regards, Hailiang
>
>> If you ask for CORR SECTion then overlapmap does just that - the CC will
>> have a certain value for each section regardless of the CHAIN
>> parameters. If you want correlation residue by residue you must ask for
>> CORR RESI
>>
>> As someone said - a lousy model will give poor CCs even if the map is
>> brilliant..
>> But once your refinement is finished it is intresting to go back and
>> check the CC of the initial maps.
>>
>> There is a belief that you need a CC of >0.5 to be able to build the
>> structure but different problems and different builders achieve
>> different results..
>> Eleanor
>>
>> Hailiang Zhang wrote:
>>> Hi,
>>>
>>> I am working on a real space correlation on a specif protein section
>>> using
>>> CCP4 OVERLAPMAP. I am using the following scripts, not sure whether it
>>> is
>>> good or not (didn't find in OVERLAPMAP documentation).
>>>
>>> overlapmap \
>>> mapin1 ${PDB}-1.map \
>>> mapin2 ${PDB}-2.map \
>>> mapin3 ${PDB}-mask.map \
>>> <<eof
>>> CORR SECT
>>> CHAIN A $START $END
>>> END
>>>
>>> There is no error message, but the results make no difference no matter
>>> how I change $START and $END. I am not sure whether the above script is
>>> ok.
>>>
>>> By the way, more importantly to me, if corr sect works at all, will it
>>> print out a single CC value by integrating over the WHOLE region define
>>> by
>>> the section range?
>>>
>>> Thanks!
>>>
>>> Best Regards, Hailiang
>>
>>
>
>
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