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Hi all, first of all, i'm not a crystallographer. I did some molecular dynamics simulations of DNA with water around it. I wanted to check the hydration patterns so i did the following: 1> I selected set of 100 snapshots taken at 5ps intervals 2> Selected only water molecules located within 3.5Å of DNA in each snapshot 3> 100 sets of individual structure factors were calculated only for the DNA in the sanpshots and average of those amplitudes treated as experimental amplitudes 4> Average of DNA coordinates of the 100 snapshots were refined against complex average structure factors using rigid, anneal, bgroup and minimize protocols of CNS. The final file minimize.pdb is the pdb file i'm using. 5> Now for water, 100 sets of individual structure factors were calculated only for the water in the sanpshots, complex average of these str. factors calculated and then using F2MTZ and FFT routines of ccp4, i got the corresponding electron density maps. If i open the map and pdb in coot, it opens fine i.e. the map is aligned on top of the pdb. But i wanted better quality pictures so tried opening them in pymol. Pymol opens them fine separately. But when i open them together, the map and pdb are on two different corners of the screen. How do i tell pymol to align the map with the pdb? Thanks for your help... Regards, Arvind
