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Coot

627 bytes added, 07:14, 10 September 2019
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[[Image:Coot-with-ATP-vector.png|400px25%|thumb|right]]
Coot is a graphics program for building, refining and analysing macromolecular models obtained with crystallographic procedures.
===Controls===
[[Image:Coot-controls-small.png|200px]]
[[morph_residues_gui.py]]
 
===Example 5: Ensemble GUI===
 
GUI to allow navigation through structural ensembles as obtained e.g. from ensemble refinement:
 
[[ensemble_plugin.py]]
==Python to Scheme and return==
A: there are 2 loop fitting tools in Coot
# C alpha -> Mainchain [http://www2.mrc-lmb.bioch.oxcam.ac.uk/personal/pemsley/coot/docweb/docs/coot.html#C_002dalpha-_002d_003e-Mainchain],[http://www2.mrc-lmb.bioch.oxcam.ac.uk/personal/pemsley/coot/docweb/docs/coot.html#Building-Links-and-Loops]# DB Loop: (No good documentation) [http://www2.mrc-lmb.bioch.oxcam.ac.uk/personal/pemsley/coot/docweb/docs/coot/protein_002ddb_002dloops.html#protein_002ddb_002dloops] Extensions -> Modelling -> DB Loop...
==LSQ superpositions==
</pre>
Untried: if you have Phenix installed: it comes with phenix.probe and phenix.reduce - you could insert the paths to these binaries into the above definitions.
 
== some symmetry mates not shown ==
 
Q: This structure has been solved and refined using phenix in the hexagonal setting of space group R 3. There is one copy per asymmetric unit in R 3. As you can see from the attached image, coot is rendering some but not all of the symmetry mates.
 
A: Turn up the radius a bit and use (set-symmetry-shift-search-size 3) . I would have thought that 2 is big enough, but maybe not in this case.

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