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. Open an mtz file with File ->Open MTZ, CIF or phs.Open pdb file of model using File->Open Coordinates.Various Procedures in Model Building using Coot
#How to install coot how to#
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).
#How to install coot software#
3 Various Procedures in Model Building using CootĬoot (Linux) is a free (for academics) model-building software used in x-ray crystallography.
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