Another cool function is the automatic rotate which can be turned on and off using the "I" key on your keyboard. Once at a residue you can move to the next residue along a chain by pressing the space bar on your keyboard. You can either directly specify the atom to jump to using the Chain, Residue Number and Atom name, or alternatively you can click on the "+" next to the different chains and then double click on a residue. To select specific residues click on Draw -> Go To Atom This will give you the following box: Difference maps contour simultaneously giving your positive and negative electron density at the same contour level (but with reversed sign!). The contour level is shown in electrons and sigma on the top of the screen. If you then click on the main display the map can be contoured using the wheel on the mouse, or alternatively using the + and - buttons on the keyboard. To contour the maps select Display Manager from the top menu and then make sure the "Scroll" box is selected for the map you wish to contour. Alternatively you can move the view around by holding down the ctrl key and left mouse button and dragging the mouse around the screen(the center of the view is indicated by a pink box). Centering can be achieved by middle-clicking on an atom. 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.
#Coot software for mac how to
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 software for mac manual
Coot is one of the best programs written over the last couple years for manual model building, and is constantly having new features added.
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