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Hi, Nian, Thanks for your reply. I figured out the problem just now. The difference indeed came from my FFT transformation. I just used all default parameters when I transform "A.mtz" to "A.map", so in the "Run FFT" dialog, F1= F, Sigma=SIGF, PHI=PHIC, Weight=Unaasigned, and I got "A.map" under these conditions. Even when I load "A.map" into Coot, the density is different with "A.mtz". But when I assigned parameters as following: F1= FWT, Sigma=Unaasigned, PHI=PHWT, Weight=Unaasigned, and ran the job, I got another "A1.map", the density is exactly same as "A.mtz" this time whatever in Pymol or Coot. I'm a rookie in this field, so herein I have another question about this: Which map should I use for showing the final density, "A.map" or "A1.map"? What's the difference of these two maps, it looks like "A.map" is much stronger than "A1.map". Really thanks for response! Zhihong 2011/1/7 Nian Huang <[log in to unmask]> > It has been discussed before. Nothing to do with FFT. Both pymol and > coot will rescale your map but differently. You have to really look > into how the programmer wrote their program to know what is going on. > For now, I suggest you just use coot map which is more realistic to > me. Also new version of pymol seems to work better. > > On Fri, Jan 7, 2011 at 1:42 PM, Zhihong Yu <[log in to unmask]> wrote: > > 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 >