This shows my ignorance about mtz files. I'm having trouble with phenix.find_helices_strands. I got 3kat.mtz from Pavel's database. I run: $ phenix.find_helices_strands 3kat.mtz labin="LABIN FP=2FOFCWT PHIB=PH2FOFCWT" and get: PHENIX find_helices_strands Wed Apr 27 13:12:19 2011 Commands: phenix.find_helices_strands 3kat.mtz labin=LABIN FP=2FOFCWT PHIB=PH2FOFCWT # find_helices_strands # # Find secondary structure in a map defined by map coeffs in an input mtz file. # Type phenix.doc for help Input map resolution is 3.1 A Labin line will be: LABIN FP=2FOFCWT PHIB=PH2FOFCWT To change it modify this by specifying FP= and PHIB= [and optionally FOM=] like this: labin="LABIN FP=2FOFCWT PHIB=PH2FOFCWT" Map from: TEMP_3kat.mtz using labin LABIN FP=2FOFCWT PHIB=PH2FOFCWT NOTE: ratio_trace_extra increased to 1.3 A as dmin > 3.0 NOTE: rad_sep_trace increased to 0.6 A as dmin > 3.0 Fixing sampling interval rad_sep_trace= 0.6 A Optimizing CA-CA tolerance to obtain ratio of 4.0 for nonamers:atoms Tracing chains at resolution of 3.1 A CCP4: Error in label assignments in LABIN
On Wed, Apr 27, 2011 at 10:43 AM, Bradley Hintze
This shows my ignorance about mtz files. I'm having trouble with phenix.find_helices_strands. I got 3kat.mtz from Pavel's database. I run: $ phenix.find_helices_strands 3kat.mtz labin="LABIN FP=2FOFCWT PHIB=PH2FOFCWT"
The labels need to actually be present in the MTZ file. The file you're using (assuming it's the same one you sent us earlier) only contains amplitudes and R-free flags. For this particular application (and phenix.fit_loops as well), you need to supply map coefficients - it won't calculate them on the fly. -Nat
participants (2)
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Bradley Hintze -
Nathaniel Echols