Dear CCP4 community,
I can't figure out how to tell Dimple to use F(+)/F(-) columns and search
for anomalous peaks.
I was trying to run dimple in the next form:
dimple -R free.mtz --anode --fcolumn F output.mtz test.pdb dimple_dir
In the output mtz I get only 2Fo-Fc and Fo-Fc maps. When I try to
u
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Dear Evgenii,
Does your input mtz file contain I(+)/I(-) and SIGI(+)/SIGI(-) columns? Dimple
runs shelxc to obtain the input reflection file for anode, which requires
anomalous intensities as input.
I.e. it essentially runs the following commands:
$ mtz2sca AUTOMATIC_DEFAULT_free.mtz anode.sca
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Dear Richard,
yes, it has I(+)/I(-) and corresponding sigmas. I tried the command you've
specified - final mtz still contains only "normal" maps but now I see
anomalous phases in anode.pha
In order to get difference anomalous maps I still have to run refmac5 with
LABIN F+=F(+) SIGF+=SIGF(+) F-=F(-)
Dear Evgenii,
it indeed makes sense to (optionally) use F+/- for refinement, but it
just hasn't been requested before and I didn't think about it myself.
I'm opening a ticket to not forget about it:
https://github.com/ccp4/dimple/issues/13
and I'll get back to it later.
Best wishes,
Marcin
On T
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Dear Evgenii,
The dimple --anode option uses AnoDe [1, 2] to calculate the anomalous
difference maps, so the anomalous map phases are in the output file anode.pha,
not in final.mtz, which is generated by refmac. You can run the script
anom-coot.sh to view the difference map in coot, or manually
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