View builder
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>Selection
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 (or [PLP]123:D) will select the residue named PLP (a ligand).
The logical operators and and 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 or, not 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.
or
What to show residue and not the domain, or vice-versa? For the full list close this, and select the appropriate focusing mode (labelled "zoom to").
Instruction
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
data-view="name_of_function".
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.
Mutate
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.