Since you mentioned phenix.cif_as_mtz, here is an even easier method that will work for most structures:
phenix.fetch_pdb --maps PDBID phenix.mtz2map PDBID.pdb PDBID_maps.mtz Caveat: this makes some assumptions about the contents of the deposition which are not always justified, also a significant fraction of the structure factor files in the PDB contain errors that will break phenix.cif_as_mtz. (Which isn't really the program's fault, since they're not actually following the CIF standard.) -Nat On Tue, May 27, 2014 at 2:06 PM, Pete Meyer <[email protected]> wrote: > Hi Patrick, > > Assuming you're talking about a model phased map: > > 1. cif -> mtz (replace PDBID as appropriate): > > phenix.cif_as_mtz PDBID.sf --use-model=PDBID.pdb \ > --output-file-name=PDBID.mtz > > 2. calculate Fc by running refmac (or cns, or phenix.refine) with 0 cycles > of refinement. > > 3. map calculation (the labin line may change depending on the program > you've used for step 2 and the map type you're looking to calculate - FWT, > PHWT are refmac coefficients for typical 2mFo - dFc ): > > fft hklin YourZeroCycleOutput.mtz mapout density_asu.ccp4 << eof > labin F1=FWT PHI=PHWT > xyzlim asu > end > eof > > Hope this helps; feel free to ask more questions if I've made things more > confused (rather than less). > > Pete > > > RiC wrote: > >> HI, >> >> Does anyone have a step by step guide to go from a structure factor file >> from the PDB to a CCP4 map (understandable to a biologist) like the one I >> can download on the electron density server? >> >> I am confused and my attempts at using CCP4 keeps coming up with "failed" >> >> Thanks >> Patrick >> >> ____________________________________________________________ >> FREE ONLINE PHOTOSHARING - Share your photos online with your friends and >> family! >> Visit http://www.inbox.com/photosharing to find out more! >> >
