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Coot: Difference between revisions
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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. | ||
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]. | 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)= | ||
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"? | ||
A: Thanks for pointing out the lack of documentation on this. I'll make a note to | A: Thanks for pointing out the lack of documentation on this. I'll make a note to add some. | ||
add some. | |||
You need to click on the torsion-general icon, then click 4 atoms that describe | 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 | |||
tree, on clicking the 4th atom a dialog will pop up with a "Reverse" button [1]. | 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? | ||
A: First, go to the | 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. | ||