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Hi,all

I refined a protein-ligand complex structure using Refmac5 and got the map coefficient "A.mtz" file. I want to represent the electron density in Pymol, so I transformed "A.mtz" into "A.map" ccp4-format map file using FFT in ccp4i (parameters are: generate "simple" map in "CCP4" format to cover "asymmetric unit", all others are default). When I load "A.map" inot Pymol and show eletron density around the ligand, I found the electron density was somewhat different comparing to that shown in coot using "A.mtz", density in Pymol (using "A.map") was much stronger than that in Coot (using "A.mtz") when showing at 1.0 sigma level. Where does the differenc come from? Should I set any other parameters when I transform mtz to map using FFT program?

Thanks in advance!

Zhihong