Thank you for your replies Randy, Pietro and Eleanor, I have just one additional question before I post a summary to ccp4bb.
I am assuming the "Disable Phase combination to remove model bias" checkbox in the ccp4i gui frontend to DM avoids the phase combination . The com file in this case reads : combine PERT nocombine . If I understand correctly this is advisable for when the DM run is started from molecular replacement derived initial phases i.e PHWTs (phases from phaser) Now I am confused as to what the labout options FCDM and PHICDM as Pietro suggested output. I ran the test and these FCDM and PHICDM values are slightly different from any of the other F's or phases. Also, the ccp4i gui uses the following coefficients to calculate a "pre-dm " and "post-dm map" when the "CREATE map file " option is checked. Pre-DM :labin F1=FWT W=FOM PHI=PHWT Post-DM: labin F1=FWT W=FOMDM PHI=PHIDM So where do the FCDM and PHICDM options come in ? I promise to put it together as a summary email for ccp4bb/public wiki once I clarify this . Thanks again. Hari Jayaram On Mon, Apr 7, 2008 at 4:46 AM, Eleanor Dodson <[EMAIL PROTECTED]> wrote: > Not real advice, but be careful if Phaser and DM use the same column > labels by default - best to assign them to something distinctive. I have had > cases where programs got confused between input and output. > > And to be safe I would run REFMAC with the output model then use the FO > PHIC FOM after a bit of refinement.. > > Eleanor > > > > > hari jayaram wrote: > > > Hi everyone, > > I have a phaser molecular replacement solution for my membrane protein > > which > > crystallized in spacegroup P3. The diffraction data is good to about 3.3 > > A. > > The model I used had 39% homology to the given protein. A solvent > > content > > analysis suggests that there probably are three dimers in the ASU ( to > > give > > about 67% solvent) > > Phaser sucessfuly found two dimers in the ASU with good density and a > > third > > dimer with very weak almost "non-existent" density. > > I am now trying to do some NCS-averaging using DM to see If I can > > improve > > the desnity for dimer 3 and have a question about the different > > co-efficients I should be using for the averaging DM run. > > > > Question1: > > The phaser output mtz file has a PHWT and a PHIC . For carrying out DM > > with > > flattening, averaging and histogram matching which phases do I use PHIC > > or > > PHWT along with observed Fo. Also for the weight do I use the FOM. > > > > Question2: > > The output mtz from DM run either way above , now has a PHIDM and a > > PHWT > > along with a FWT and FC. Which coefficients should I be using to get a > > map > > after DM for building. > > > > FWT and PHWT > > or > > Fo and PHIDM > > or > > FWT and PHIDM. > > > > > > Thank you for your help > > Hari > > > > > > > >
