Hi Zhihong -
You should use 'FWT' and 'PHWT'. These are the sigma-A weighted 2Fo-Fc map coefficients (likewise, 'DELFWT' and 'PHDELWT' are the sigma-A weighted Fo-Fc map coefficients). The sigma-A weighted 2Fo-Fc map (also known as the mFo-DFc map) has become the standard electron density map to use for model building and for paper figures (unless you're using CNS or Phenix, where you might use a composite-omit version of the same map). Using the 'F' and 'PHIC' coefficients will produce a simple Fo map phased by the model phases; this is generally considered to be more model biased than the sigma-A weighted maps. However, I'm not sure if you're doing the right thing by leaving SIGF unassigned. I believe this should be assigned to the experimental error, which is usually called 'SIGF' in your mtz file. I don't know if FFT actually uses this for anything when it's calculating your map file. I'm also not sure what you should use for the weight parameter - perhaps 'FOM'? I should also point out that you can ask Refmac to output the sigma-A weighted 2Fo-Fc and Fo-Fc maps automatically at the end of a refinement run. If you're using the ccp4i GUI, expand the "Monitoring and output options" section of the Refmac window, and check the box marked "Generate weighted difference maps..." Then you don't need to mess around with FFT at all. Hope that helps (and I hope I didn't make any egregious mistakes there!), Matt -- Matthew Franklin, Ph. D. Senior Research Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (646) 275-7165 _____ From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Zhihong Yu Sent: Friday, January 07, 2011 4:31 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] The density shown in Pymol and Coot is different. 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 <huangn...@gmail.com> 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 <nkyuz...@gmail.com> 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
