![]() ![]() You can zoom in and out by using the right mouse button. Once you have loaded your coordinates, 2Fo-Fc and Fo-Fc maps the screen should look something like this:Ĭarbon atoms are coloured yellow, nitrogen's blue, oxygen's and waters red, 2Fo-Fc density dark blue, Fo-Fc positive density green and negative density red.Ĭoot uses a live mouse which lets you rotate the image by holding down the left mouse button and moving the mouse around the graphics window. ![]() map To convert maps from cns or shelx (omap) formats use the usf program "mapman" e.g.: ![]() The map file has to be in ccp4 format and have the extension. If you are not using Refmac and need to load a separate map file, select: Just selecting "Is a Difference Map" will not generate an Fo-Fc difference map - make sure you make the appropriate selection for Amplitudes and Phases! To load your Fo-Fc map simply repeat this procedure BUT select DELFWT and PHDELWT for the Amplitudes and Phases, and then make sure the "Is a Difference Map" box is selected. If you want to load a 2Fo-Fc map just click OK. You will next get a box that looks like this: (I think you can select fcf if you have run shelx but I haven't checked this). If you are using Refmac you can next load the mtz file by selecting: To load your pdb file use the mouse to select:Īnd then simply double click on the pdb file which should open in the main graphic window. You can look through the tips if you like however I normally just close this box. Setccp4 (necessary to load the refinement dictionaries)Ĭoot will then open and often give you a little tip box such as: Alternatively you can generate various map files from CNS, SHELX or the ccp4 FFT program and read these in separately. If you are using Refmac for refinement coot can directly read your mtz file as Refmac adds phase information to the file. ![]() The best way to learn how to use Coot is to experiment yourself, however the following should provide some hints and tips I have found useful.Ĭoot allows you to manually change your pdb file based upon experimental electron density. It is written by Paul Emsley who has also provided a helpful website with both a FAQ and a wiki. Coot is one of the best programs written over the last couple years for manual model building, and is constantly having new features added. ![]()
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |