Hi Folks I have a query regarding the difference map between the two structures ligand bound data (2.5A) and native (2.8A). I tried to calculate the fourier difference map between two data sets ligand bound- native. The protocol in CCP4 that i used is as: 1.merge the mtz file of native nad ligand bound using cad 2. scaling this combine file with scaleit program followed by map generation uisng fft.
I got the map but i did not find the fu;ll map of the ligand,i can only see small density nera the ligand binding site at 5 sigma level. I have calculated omit map that cleraly showed the ligand. why is such discrepency in the two cases, is there is something missing from the calculation. kindly help me out. Thanks and regards Intekhab alam -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL
