Hi Martin, I followed your instructions and everything works. Thank you for your illustration!
On Mon, Mar 20, 2017 at 3:52 AM, Martin Montgomery <m...@mrc-mbu.cam.ac.uk> wrote: > Hello, > > You need to tell pymol what to do with the map. > > Load your pdb file > Load the map > > create an object with residues you wish to display the map around. You > can use the create command to do this or you can click on all the residues > that you want to use in the main window then go to the object called (sele) > in the right hand sidebar, click A and then copy to object. This will > create an object called obj01 with the selected residues. You can rename > this if you wish. > > Then you need to use the isomesh command to display the map. > > > isomesh mapname, mapfilename.ccp4, 2.5, obj01, carve=2.0 > > mapname is the name you want to appear in the right hand sidebar for the > mesh (can be the same as the mapfilename if you wish) > > mapfilename would be D83Vchimmap1 (from your screen shot). > > 2.5 is the sigma setting and carve=2.0 means the mesh is created within > 2.0 Å of the selected atoms. Adjust these values to suit. > > You might want to go back to go back and check your FFT log and look at > the grid settings. It is a good idea to re run the FFT job but double the > grid values from the original job. > > It is all covered here: > > https://pymolwiki.org/index.php/Display_CCP4_Maps > > Regards > > MGM > > Martin G Montgomery > ATP Synthase Group > Medical Research Council Mitochondrial Biology Unit > University of Cambridge > Wellcome Trust/MRC Building > Cambridge Biomedical Campus > Hills Road > Cambridge > Great Britain > CB2 0XY > > www.mrc-mbu.cam.ac.uk > > > > > > > On 18 Mar 2017, at 10:43, Eleanor Dodson <eleanor.dod...@york.ac.uk> > wrote: > > I think CCP4MG does this very selectively? > > Eleanor Dodson > > On 17 March 2017 at 17:03, Xiao Lei <xiaolei...@gmail.com> wrote: > >> Dear All, >> >> Thanks for the information. >> I tried the way suggested by pymol wiki, but pymol fail to display the >> map. >> This is what I did: Run Fft to generate simple mapin ccp4i, input mtz map >> from refmac, set F1=FWT and PHIC=PHWT, Sigma=SigF, Weight=FOM. Add the >> file extension .map.ccp4 to the generated output map. After open by pymol, >> only a unit cell sign is shown (I attach here), no map is displayed.. I >> use Pymol 1.8.X in Win7. >> >> Any further input is appreciated. >> >> >> >> .<Fftmap.PNG> >> >> >> >> >> On Fri, Mar 17, 2017 at 7:41 AM, Xiao Lei <xiaolei...@gmail.com> wrote: >> >>> Dear All, >>> >>> In Coot, I could adjust the densities of map (2Fo-Fc in my case) radius, >>> but I'd like to show the density on selective residues, not on the >>> unselected part of structure, is there a way to do it? I am using WinCoot >>> 0.81. >>> >>> In addition, could Pymol do it? >>> >>> Thanks ahead! >>> >> >> > >
