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Hi, > 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: Well, I'm not a molecular dynamicist (if that's a word)... > 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? 1. Coot (I presume, still haven't found time to get the build process working) uses symmetry operators to expand the map to cover a region (probably around the active center, or model center of gravity). Pymol does not, so you'll have to use mapmask to extract a region covering your model. 2. It's probably better to post pymol questions to the pymol mailing list. Good luck, Pete Pete Meyer Fu Lab BMCB grad student Cornell University
