[buster-discuss] test flag number in BUSTER

[David Veesler]

Hi Keitaro,
if you have a look to the various plot generated by Buster you will see that the contribution of the solvent is significative up to 5A thus it depends on what you call low resolution :)
Concerning the gap Rfree-R, you can get an estimation of the refinement behavior on the Buster wiki http://www.globalphasing.com/buster/wiki/index.cgi?AutoBusterExample1osgBasicNCS
Best
David

> Dear David (and BUSTER developers),
> 
> Thank you for your reply.
> 
> Do you mean BUSTER always use flag number 0 if FreeR_flag column
> present in the mtz file, right?
> 
> If so, in my case the flag was correctly chosen.
> 
> 
> I have still some questions:
> 
> - If superior bulk solvent model helped, I think it should improve
> R-factors in low resolution shell.
>  But actually, rather high resolution shell got improved.
> 
> - Sorry I correct these values 42% and 35%, respectively:
>> Looking at free-R value given by autoBUSTER, I noticed it is very
>> smaller than by other softwares (phenix.refine and refmac5 say 43%,
>> but BUSTER says 36%).
> 
> And here's summary:
> 
>              Rwork/Rfree    after refinement (5 macro cycles)
> BUSTER        30/35       -> 34/35
> phenix.refine 35/42
> 
> - It means R-free by BUSTER is approximately equal to R-work by phenix.refine.
> This is why I doubted test flag was wrongly chosen.
> 
> - And after BUSTER refinement cycles, R-work is getting higher,
> finally, R-work and R-free reached similar values.
> Since difference between R-work and R-free is very small -- I think
> something is wrong with my input.
> 
> 
> I will appreciate any comment,
> 
> Keitaro
> 
> 
> 
> 2011/3/27 David Veesler <david.veesler at afmb.univ-mrs.fr>:
>> Hi Keitaro,
>> I am not a Buster developer but a thorough user and can provide you with some answers.
>> When you start a Buster job, you can see on the shell that Buster carries on a basic check of your pdb and mtz and directly after you can see something like that
>> 
>> ##############################################################################
>> # refining against FP,SIGFP with: FreeR_flag
>> ##############################################################################
>> 
>> In that case it means that Buster runs with a FreeRflag:
>> -the one present in your mtz if you have one with the correct name and 0 label
>> -or with an automatically generated one with 5% of your reflections if you don't have one matching these criteria
>> 
>> Regarding your Rfree values, there is nothing surprising at all, Buster always provide better Rfree values than other refinement software and this is due in a large extent to the superior solvent model. Accordingly, if you compare the electron-density maps you will see that they are of superior quality with Buster.
>> 
>> HTH
>> Cheers
>> David
>> 
>> Le 26 mars 2011 à 08:02, Keitaro Yamashita a écrit :
>> 
>>> Dear BUSTER developers,
>>> 
>>> I have questions about running autoBUSTER 2.8.
>>> I'm very new to this software.
>>> 
>>> How can I know which FreeR_flag number is used as test set?
>>> And how can I tell BUSTER the correct flag number?
>>> 
>>> Looking at free-R value given by autoBUSTER, I noticed it is very
>>> smaller than by other softwares (phenix.refine and refmac5 say 43%,
>>> but BUSTER says 36%).
>>> So I'm afraid that free-R flag number was wrongly chosen.
>>> 
>>> 
>>> Thanks in advance,
>>> 
>>> Keitaro
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