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
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 [email protected] 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: [email protected] 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
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 [email protected] 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: [email protected] 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 [email protected] 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: [email protected] 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
participants (2)
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Peter Grey -
Tom Terwilliger