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Coot: Difference between revisions
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[[Image:Coot-with-ATP-vector.png|400px|thumb|right]] | [[Image:Coot-with-ATP-vector.png|400px|thumb|right]] | ||
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]. License 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)= | ||
Q: | ==NCS edits== | ||
I am sure this exists somewhere through scripting in COOT, but can I apply NCS edits to only a subset of NCS copies? In other words, can I tell coot which are NCS related chains, and which aren't. I am working on this nightmarish case of asymmetrical homodimers, where the sequences are very similar, but the structures are not, so I need to tell coot which chains are actually related to each other. | Q: I am sure this exists somewhere through scripting in COOT, but can I apply NCS edits to only a subset of NCS copies? In other words, can I tell coot which are NCS related chains, and which aren't. I am working on this nightmarish case of asymmetrical homodimers, where the sequences are very similar, but the structures are not, so I need to tell coot which chains are actually related to each other. | ||
A: Nightmare. If you have a recent [1632 or later for the scheme version, 1646 for the python version] Coot, you can do this: | A: Nightmare. If you have a recent [1632 or later for the scheme version, 1646 for the python version] Coot, you can do this: | ||
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There is also a GUI to activate this feature under Extensions -> NCS. | There is also a GUI to activate this feature under Extensions -> NCS. | ||
==SHELXL== | |||
Description of problematic situation: I am using [[SHELXL]] to refine my 1.2 Å data and I am refining the hydrogen atoms. Subsequent rebuilding in coot is difficult though since hydrogens often does not "follow" when you do side chain rebuilding. For the moment I have quit transfering hydrogens to coot and add the hydrogens every refinement cycle, though it would be good I think if I could see them in coot without bothering about wrong positions. So these are my specific questions: | Description of problematic situation: I am using [[SHELXL]] to refine my 1.2 Å data and I am refining the hydrogen atoms. Subsequent rebuilding in coot is difficult though since hydrogens often does not "follow" when you do side chain rebuilding. For the moment I have quit transfering hydrogens to coot and add the hydrogens every refinement cycle, though it would be good I think if I could see them in coot without bothering about wrong positions. So these are my specific questions: | ||
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A: Yes this fails. Hydrogens are named differently to SHELX hydrogens. In principal this could be made to work if the dictionary was reworked to use SHELX hydrogen names. This would also fix the chi angles problem too of course. | A: Yes this fails. Hydrogens are named differently to SHELX hydrogens. In principal this could be made to work if the dictionary was reworked to use SHELX hydrogen names. This would also fix the chi angles problem too of course. | ||
==Image quality on NVidia cards== | |||
Q: improvement of image quality on machines with NVidia cards? | Q: improvement of image quality on machines with NVidia cards? | ||
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- | ==Setting default to show symmetry-related molecules== | ||
Q: How to set the default to display symmetry related molecules? | Q: How to set the default to display symmetry related molecules? | ||
A: Add (set-show-symmetry-master 1) to the appropriate file. | A: Add (set-show-symmetry-master 1) to the appropriate file. | ||
==Startup files== | |||
Q: I still have a ".coot" file in my home folder for a few coot preferences that I couldn't find in the new ".coot-preferences/coot-preferences.scm". There is a warning that I should not add commands to this file. So is a "~/.coot" still the proper place to add default commands for coot? | Q: I still have a ".coot" file in my home folder for a few coot preferences that I couldn't find in the new ".coot-preferences/coot-preferences.scm". There is a warning that I should not add commands to this file. So is a "~/.coot" still the proper place to add default commands for coot? | ||
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So you have a variety of places. Personally I mostly use ~/.coot. | So you have a variety of places. Personally I mostly use ~/.coot. | ||
==Torsion general== | |||
Q: How do I use "torsion general"? | Q: How do I use "torsion general"? | ||
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the "Reverse" button should invert the moving and "base" part of the residue. | the "Reverse" button should invert the moving and "base" part of the residue. | ||
==Peak heights in maps== | |||
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? | ||