Coot will process this request (takes a while, ~3min) and spits out a mainchain configuration if it can. residue#2 and #10 that you want to have converted in mainchain atoms. In Model/Fit/Refine, choose Ca Zone->Mainchain.Keep building the Ca frame until there is no clear direction on where to add Ca atom.When you're satisfied with the baton, click "Accept". You can also lengthen/shorten the baton with the appropriate options. CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. You can change where the 2nd Ca is by choosing "Try Another" in the Baton window. This builds a Ca atom at the crosshair and connects that to another point 3.8A (distance of Ca-Ca) away. Put the crosshair in the Canvas to a skeleton point where a continous polypeptide chain could be observed in the map.The skeleton will serve as a guide of where to build atoms. This procedure creates a skeleton (points and connection) in the map. You can "Color and Prune", to delete possible side chain points so your skeleton looks cleaner. In the Skeleton Dialog window, turn skeleton mode On (this will display the skeleton). The 2Fo-Fc map is usually colored blue and the Fo-Fc map is colored green (positive density) and red (negative density). Now you should see both model and map in the Canvas.To make an Fo-Fc map, use DELFWT and DELPHWT To make a 2Fo-Fc map, use the FWT and PHWT. This will pop up a dialogue window for map calculation.
You need to download either Coot (in Linux) or WinCoot (in Windows) and install these.įollow the links below on how to download and install these programs. Pymol, SwissPDB Viewer, or Molscript/Raster3D.Ĭoot is NOT a crystallographic refinement program. There are plenty of programs for that purpose eg. I found Coot to be easy to learn and more user-friendly than other model-building programs such as O or XtalView.Ĭoot is NOT a molecular graphics program (ie programs for making pretty pictures for publications).
3 Various Procedures in Model Building using CootĬoot (Linux) is a free (for academics) model-building software used in x-ray crystallography.