[phenixbb] Calculate F (model) + Calculate Map Correlation

[Pavel Afonine]

As a remark, CC alone is not a very good metric. It may give you a very 
high value (=good!) for very weak or negative density values, because it 
is scale independent. Better is to use CC and map value(s). For 
modeling/automation purposes I usually use a triplet (CC, 2mFo-DFc, 
mFo-DFc) of values, where the last two are map values per atom or per 
fragment in question. Of course it all depends on what exactly goal you 
are trying to achieve.

Pavel

On 6/18/14, 1:04 AM, Tim Gruene wrote:
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> Dear George,
>
> people already explained in detail on ccp4bb why you should be
> cautious about what you are planning to do. That's certainly the
> reason why you are having trouble finding the right software tool for
> your purpose: Your approach may be wrong.
>
> If you still insist, you may have to program your own code. You find a
> simple example for how to calculate a CC of a model against a map in
> the function Molekel:mapCC in file 'molekel.cpp' of the source code of
> knuspr (http://shelx.uni-ac.gwdg.de/~tg/research/programs/knuspr/).
>
> Be reminded that the CC of a modified ligand calculated against the
> original map is quite meaningless.
>
> Cheers,
> Tim
>
> On 06/17/2014 08:22 PM, George Devaniranjan wrote:
>> Hi,
>>
>> I am trying to use phenix and I was trying to do the following:
>>
>> Take a PDB, generate a MTZ file using Calculate F (model) and lets
>> call it
>>
>> native.mtz
>>
>> then change a few phi and psi values of the pdb (so its slightly
>> different from the native), run Calculate F (model)
>>
>> model.mtz
>>
>> Now I tried to calculate the CC of the two MTZ using Calculate Map
>> Correlation.
>>
>> I get the following:
>>
>> "Missing at least one map file or label"
>>
>> What am I doing wrong?
>>
>> Thank you, George
>>
>>
>>
>> _______________________________________________ phenixbb mailing
>> list phenixbb at phenix-online.org
>> http://phenix-online.org/mailman/listinfo/phenixbb
>>
> - -- 
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
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