Merry Christmas!The content of this page was edited by matteoferla on the 2021-09-27 15:40:12.070024.
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The ornaments are repo for notes and files) by doing protein design recklessly, i.e. without any positive controls and without checking a single free-energy score. Please do not synthesise it at home!, while . This tree was generated from scratch using Rosetta and PyMOL (see
This protein view was generated using Michelanglo.
Proteins are chains of L-amino acids linked via their backbone atoms (carboxyl and amine of the α carbon). This sequence of backbone atoms is represented by the (green) ribbon-like structure.
When the backbone atoms hydrogen-bond with each other in a consistent way secondary structure arises.
α-Helices are represented as spirals, while β-sheets appear as adjecent flat strands.
Some residues of interest are represented as ball and sticks like akin to an old chemistry set. In these representations the atoms are colour-coded based on the element. Carbon can be any colour, while nitrogens are in blue, oxygens are in red, hydrogens in white, sulfurs in yellow and phosphorous in orange. The latter is found as phosphate groups so will appear as a distinctive red-tipped orange tetrahedral end of a sidechain. Ions are represented by a variety of colours. But are generally represented as spheres of the correct atomic radius.
This tool allows you to create custom anchor elements that control the protein. See documentation for more.
<span class="prolink" data-toggle="viewport">Change a setting!</span>
Option A. Selection language
For more information on the NGL selection language see NGL manual
This controls the residues to focus on. The selection uses the NGL selection language.
1:A will select residue 1 of chain A,
1-20:B the residues 1 to 20 of chain B,
* for everything,
[PLP]123:D) will select the residue named PLP (a ligand).
The logical operators
or can also be used, e.g.
:B or :C will select chains B & C. You can only select residues that exist in the structure, if not it will either show all or erroneously pan off camera when manually written. In this builder you will not be allowed to.
Also to prevent memory issues in mobiles the limit, in the builder only, for residue mode is 500 atoms.
To select two different elements use the logical operator
and, because you want to select anything that matches X or Y.
Option B. Build Selection
The following is simpler, but much more limited that the previous.
Add structure from another pages
A single page can support multiple models, which can be toggled via
data-load in the prolink (a link that control the protein view).
To show a structure, two pieces of information are needed:
- one is the structure, namely the information of each atom (e.g. element, residue, coordinates). The PDB file basically.
the other is the representation, namely the combination of the orientation, residues shown, colors and field of view etc. In the case of PyMOL generated views,
these are functions that can be called via the attribute
To combine two PyMOL representation of the same structure use the
add representation only button: there is no need to slow things down by loading the same coordinates, else add both.
This applies also to cases where the structure is taken remotely (e.g. PDB database).
Note that editing the JS in blocked for regular users (due to security concerns), please speak to the site admin if you would like to alter your permissions. Also note that this page will refresh in order for the changes to be made.
Create a second structure where a set of amino acids are replaced using PyMOL's mutagenesis algorithm. This will alter only the side chain of the residues mutated and does not repack the neighbouring sidechains nor does it account for blackbone torsion. Note that this page will reload for the changes to be made, so make sure you have saved the edits to the text beforehand.
View builder for loading
This tool allows you to alter the initial view of the protein that is seen once it is loaded. See documentation for more.