Added functions to color model by map/model correlation (only works for P1 map/mtz right now, uses phenix.map_model_cc), color by protein/nucleic acid, and options to restrict coloring to just the active chain.
https://www.dropbox.com/s/0b4bebwxw0p9x0e/oli_custom.py?dl=0
Cheers
Oli
On Wed, 20 Jul 2016 18:02:15 +0100, Oliver Clarke <[log in to unmask]> wrote:
>Also, here is a little screen recording showing the use of a couple of these functions:
>
>https://www.dropbox.com/s/92mra1c1fpsf77n/coot_custom_coloring_small.mov?dl=0
>
>Cheers
>Oli
>
>On Wed, 20 Jul 2016 14:39:48 +0100, Oliver Clarke <[log in to unmask]> wrote:
>
>>Hi all,
>>
>>Paul just added a very useful set of functions to the Coot API (only in the very latest nightlies - r6174 or later) that allow custom coloring of models.
>>
>>Taking advantage of these, I've written a few different coloring options into my custom setup (https://www.dropbox.com/s/0b4bebwxw0p9x0e/oli_custom.py?dl=0).
>>
>>If you have my extensions installed, you can find these under Custom...Display.
>>
>>Three functions allow coloring by residue identity:
>>These allow coloring hydrophobic and polar residues in distinct colors, coloring positive and negatively charged residues differently, or highlighting a specific subset of residues via an entered string (e.g. fyw or FYW will color Phe, Tyr and Trp).
>>
>>And three functions are present for coloring by validation statistics:
>>Color rotamer outliers and residues with missing atoms (highlighted in distinct colors); Color ramachandran outliers; and color CaBLAM (C-alpha dihedral geometry) outliers. The two latter functions require phenix, sed and awk to be accessible from the command line. As I'm using phenix.ramalyze to detect the Rama outliers these might not match up exactly with those on the plot in Coot, but hopefully they are useful anyway. The colors won't update automatically upon model alteration, so if you want to refresh them just run the desired command again.
>>
>>To cycle between the user-defined representations and other representation modes, use the keys "]" and "[" to cycle forward and back respectively.
>>
>>Cheers,
>>Oli.
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