Thanks Patrick for your question. I too have a similar problem. I used CCP4 uniqueify to generate a MTZ file then used FFT to convert it to a CCP4 map. But it looks nothing like the map from the server.
I will let you know if I figure it out. On Tue, May 27, 2014 at 5:15 PM, Nat Echols <[email protected]>wrote: > 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! >>> >> >
