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 <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 <[email protected]> wrote: > > I think CCP4MG does this very selectively? > > Eleanor Dodson > > On 17 March 2017 at 17:03, Xiao Lei <[email protected] > <mailto:[email protected]>> 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 <[email protected] > <mailto:[email protected]>> 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! > >
