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Coot is a graphics program for building, refining and analysing macromolecular models obtained with crystallographic procedures.
 
Coot is a graphics program for building, refining and analysing macromolecular models obtained with crystallographic procedures.
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There is a [http://www.biop.ox.ac.uk/coot/ homepage] with extensive [http://www.biop.ox.ac.uk/coot/docs.html documentation]. The program may be downloaded for Linux, Mac and Windows computers from the [http://www.ysbl.york.ac.uk/~emsley/software/binaries/ primary server] or, if that is not available, from an [ftp://turn5.biologie.uni-konstanz.de/ external mirror]. License is GNU GPL.  
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There is a [http://www.biop.ox.ac.uk/coot/ homepage] with extensive [http://www.biop.ox.ac.uk/coot/docs.html documentation]. The program may be downloaded for Linux, Mac and Windows computers from the [http://www.ysbl.york.ac.uk/~emsley/software/binaries/ primary server] (as of July 10, 2009 there's a new site at http://www.biop.ox.ac.uk/coot/devel/build-info.html) or, if that is not available, from an [ftp://turn5.biologie.uni-konstanz.de/coot external mirror]. The license of Coot is GNU GPL.  
    
=Installing Coot=
 
=Installing Coot=
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=Assorted questions and answers (from the mailinglist)=
 
=Assorted questions and answers (from the mailinglist)=
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It should be noted that the answers ("A") are from Paul Emsley himself (and were maybe slightly edited).
    
==NCS edits==  
 
==NCS edits==  
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Q: How do I use "torsion general"?
 
Q: How do I use "torsion general"?
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A: Thanks for pointing out the lack of documentation on this. I'll make a note to
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A: Thanks for pointing out the lack of documentation on this. I'll make a note to add some.
add some.
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You need to click on the torsion-general icon, then click 4 atoms that describe
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You need to click on the torsion-general icon, then click 4 atoms that describe the torsion - the first atom will be the base (non moving) part of the atom tree, on clicking the 4th atom a dialog will pop up with a "Reverse" button [1].
the torsion - the first atom will be the base (non moving) part of the atom
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tree, on clicking the 4th atom a dialog will pop up with a "Reverse" button [1].
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Move this dialog out of the way and then left mouse click and drag in the main
Move this dialog out of the way and then left mouse click and drag in the main
   
window will rotate the moving/"top" part of the residue round the clicked atoms
 
window will rotate the moving/"top" part of the residue round the clicked atoms
 
2 and 3.  When you are happy, click "Accept".
 
2 and 3.  When you are happy, click "Accept".
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Q: I have some peaks in my map which take water or sodium/magnesium or chlorine atom with out giving out any positive or negative density upon further refinement. Is there any easy way of calculating the peak height / number of electrons at a given position, say a mouse click point in coot? Is there any formula to calculate the number of electrons based on sigma level and peak height, as given in difference map peaks in coot?
 
Q: I have some peaks in my map which take water or sodium/magnesium or chlorine atom with out giving out any positive or negative density upon further refinement. Is there any easy way of calculating the peak height / number of electrons at a given position, say a mouse click point in coot? Is there any formula to calculate the number of electrons based on sigma level and peak height, as given in difference map peaks in coot?
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A: First, go to the coot wiki and pick up the scheme key bindings.  
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A: First, go to the Coot wiki and pick up the [[Coot#Scheme_Scripts|scheme key bindings]].  
    
If you want density information at a given cursor point: point at the blob, press the 'g' key (which recentres on the biggest density under the cursor).
 
If you want density information at a given cursor point: point at the blob, press the 'g' key (which recentres on the biggest density under the cursor).
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  (apply density-at-point (imol-refinement-map) (rotation-centre))
 
  (apply density-at-point (imol-refinement-map) (rotation-centre))
 
There is no user access to the peak integration code of coot as yet.
 
There is no user access to the peak integration code of coot as yet.
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It should be noted that the answers ("A") are from Paul Emsley himself (and were maybe slightly edited).
 
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