3/9/2023 0 Comments Color residues jmol![]() Once open, go to the command line in PyMOL and enter ‘run colour.py’ (or subbing in whatever you’ve called your file). Then, from the same directory as this new file, open PyMOL with any suitable structure. You can call it whatever you like, as long as it has ‘.py’ at the end. You can see in the script that every residue has its own unique colour, with names as imaginative as ‘deepsalmon’, ‘smudge’ and ‘wheat’ (whether or not Theresa May keeps a high tyrosine diet is beyond the scope of this blog post).Ĭopy the text and paste into a new file called – for example – ‘colour.py’. # COLOUR BY RESIDUE - PATRICK BRENNAN, UNIVERSITY OF OXFORD - AUGUST 2020Ĭmd.select ('backbone_carbons','name C+CA')Ĭmd.select ('ALA','name CB and resn ALA')Ĭmd.select ('ARG','name CB+CG+CD+CZ and resn ARG')Ĭmd.select ('ASN','name CB+CG and resn ASN')Ĭmd.select ('ASP','name CB+CG and resn ASP')Ĭmd.select ('CYS','name CB and resn CYS')Ĭmd.select ('GLN','name CB+CG+CD and resn GLN')Ĭmd.select ('GLU','name CB+CG+CD and resn GLU')Ĭmd.select ('HIS','name CB+CG+CD2+CE1 and resn HIS')Ĭmd.select ('ILE','name CB+CG1+CG2+CD1 and resn ILE')Ĭmd.select ('LEU','name CB+CG+CD1+CD2 and resn LEU')Ĭmd.select ('LYS','name CB+CG+CD+CE and resn LYS')Ĭmd.select ('MET','name CB+CG+CE and resn MET')Ĭmd.select ('PHE','name CB+CG+CD1+CD2+CE1+CE2+CZ and resn PHE')Ĭmd.select ('PRO','name CB+CG+CD and resn PRO')Ĭmd.select ('SER','name CB and resn SER')Ĭmd.select ('THR','name CB+CG2 and resn THR')Ĭmd.select ('TRP','name CB+CG+CD1+CD2+CE2+CE3+CZ2+CZ3+CH2 and resn TRP')Ĭmd.select ('TYR','name CB+CG+CD1+CD2+CE1+CE2+CZ and resn TYR')Ĭmd.select ('VAL','name CB+CG1+CG2 and resn VAL')Ĭode = This, I felt, had two advantages: firstly, it allows the viewer to easily pick out the trajectory of the backbone when the side chains are all visible and secondly it highlights glycine’s role as a ‘blank’ amino acid that has no side chain to speak of, as it blends into the overall backbone. Secondly, whilst the NGL Viewer option colours the backbone portion of every residue the same as the side chain, and colours glycine (which is just the backbone) as white, I decided to colour the backbone region of every residue as white. Firstly, whereas in the NGL Viewer option every atom in the residue was coloured the same, I decided to keep the heteroatoms (oxygen, nitrogen and cysteine) as their standard colours (red, blue and yellow respectively). With this in mind I decided to write a script to colour residues in PyMOL according to a similar colour scheme – with two important differences. leucine and isoleucine are slightly different shades of green), allowing for both easy identification of residue type and easy inspection of the overall geography of a protein structure: for instance, similarly blue-coloured lysines and arginines are often seen on the outskirts of the protein, whilst the core is often a mix of greens (leucine and isoleucine) and grey (phenylalanine). This setting assigns a unique colour to every residue such that similar amino acids have similar but distinguishable hues (e.g. one colour for hydrophobic, one for hydrophilic, one for positively charged, one for negatively charged), but the best I had encountered so far was the ‘colour by residue’ option in NGL Viewer – previously the default viewer option on the RCSB Protein Data Bank’s website. Looking online I found a few scripts which loosely coloured residues according to properties (e.g. Whist you can easily differentiate atom types based on colour in the colour menu, and even choose which colour you wish carbons to show up as whilst keeping heteroatoms different colours, this assigned carbon colour would be constant throughout the entire protein. However one thing I felt that PyMOL lacked was an easy way to visually distinguish residues based on type. – which all have their own pros and cons. It allows you to toggle between different representations of the protein – such as cartoon, surface, sticks, etc. PyMOL is a handy free way of viewing three dimensional protein structures.
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