[phenixbb] RESOLVE question

Tom Terwilliger terwilliger at lanl.gov
Thu Oct 1 12:05:16 PDT 2009


Hi again Peter,

I forgot to mention in the previous email that in a prime and switch  
run of resolve there is a place to input FCALC:
hklin sigmaa.mtz
labin FP=FP FC=FC PHIC=PHIC FOM=WCMB FWT=FWT
All the best,
Tom T

On Oct 1, 2009, at 10:43 AM, Tom Terwilliger wrote:

> Hi Peter,
>
> If I understand the question correctly, then I think you want to:
>
> 1. use experimental data only (including MAD/SAD phases and HL  
> coeffs if available) as input to resolve with
>
> hklin my_experimental_data_only.mtz
> labin FP=FP SIGFP=SIGFP PHIB=PHIB FOM=FOM
>
> (skipping PHIB and FOM if you have only FP and SIGFP and no  
> experimental phases
>
> 2.  You can optionally use your model map as a starting map for  
> resolve with:
>
> hklstart 2fofc.mtz
> labstart FP=2FOFCWT PHIB=PH2FOFCWT
>
> I don't think there is any time where you would want to use FMODEL  
> or FCALC as input to resolve, though I could be wrong on that!
>
> All the best,
> Tom T
>
>
> On Oct 1, 2009, at 9:37 AM, Peter Grey wrote:
>
>> Hello,
>>
>> We use iterative cycles of manual building (coot) - refinement  
>> (phenix) - density modification to improve maps for the next  
>> building step (RESOLVE).
>>
>> Should we use FMODEL,PHIFMODEL from phenix or FCALC,PHIFCALC in the  
>> input to RESOLVE.  MODEL structure factors are closer to  
>> experimental ones but are they better for density modification  
>> purposes ?
>> I think that if the program uses , as in DM, only Fobs and phases  
>> to calculate the maps then  PHIFCALC is better (no contribution of  
>> solvent) but if the programs calculates 2Fo-Fc maps then  
>> FMODEL,PHIFMODEL is better since it was shown that these maps are  
>> beter when bulk solvent correction is used.
>>
>> Could you please comment whether this reasoning is correct and give  
>> information as to which is the case in resolve.
>>
>> Thanks,
>> -- 
>> Peter
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
>
> Thomas C. Terwilliger
> Mail Stop M888
> Los Alamos National Laboratory
> Los Alamos, NM 87545
>
> Tel:  505-667-0072                 email: terwilliger at LANL.gov
> Fax: 505-665-3024                 SOLVE web site: http:// 
> solve.lanl.gov
> PHENIX web site: http:www.phenix-online.org
> ISFI Integrated Center for Structure and Function Innovation web  
> site: http://techcenter.mbi.ucla.edu
> TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
> CBSS Center for Bio-Security Science web site: http://www.lanl.gov/ 
> cbss
>
>
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb


Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss




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