Here we will try to show you how to make specific representations, by the user selection part of the form.
The first example will use the pdb code 1CRN (CRAMBIN).
Set the title to "1CRN Cysteine" and display the backbone as "Spline". Choose the t_spheresky2 for the background and increase the image size to normal (500x500). And finally go to the supplementary representation part. Here you can define specific selections in the protein and how to represent them. For our first test, we just want to show all the cysteines of the crambin. For that purpose we will simply set "selection1" to rname=CYS. This will specify to dino to render independently all the cysteine residues. By default the representation is set to BallnStick color by Atom. We will keep the default for the example. Now that the form is ready, the rendering can be launched via the process button. Note that all the options are displayed in the waiting page. The result is presented here (after ~1mn):
Here you can find other examples with the according option:
Spline backbone color by secondary Structure
Image Size Big(700x700)
Chains All: Xrot 0. Yrot 90. Zrot 0.
Selection1 : rname=CYS display as BallnSticks color yellow
Selection2 : rname=LYS display as BallnSticks color by aliceblue
Selection3 : rnum=15 display as Sphere color gold
Light : SkySpot
Time : ~2mn
Title 1CRN selection skylight
backbone render as Spheres color grey
side chains render as Spheres color grey
selection1 rname=CYS render as None color by yellow
selection2 rname=PRO render as None color by red
selection3 rnum=15:18 render as None color by blue
background t_box size 700x700
Time : ~7mn
triose phosphate isomerase dimer
surface opacity 0.30 color white
Selection1 chain=A render as Spline color by Secondary structure
Selection2 chain=B render as BallnSticks color by Class
Background t_spheresky2 size 700x700
Time : ~38mn
This high time consuming is due to the surface.
For comparison look at the gallery page.
We made the same picture without surface (1mn),
then with surface but opacity at 1.0 (1.5mn), and in order to improve the view,
the camera was set to ultra-wide.
user selection 1 rnum=1:329 and chain=C render as Spline color by blue
user selection 2 rnum=380:714 and chain=C render as Spline color by red
user selection 3 rnum=1697:2020 and chain=C render as Spline color by green
user selection 4 rnum=2021:2171 and chain=C render as Spline color by lightblue
user selection 5 rnum=2172:2332 and chain=C render as Spline color by yellow
user selection 6 rnum=517:527,558:565,712,1811:1818 and chain=C render as Spheres color by white
user selection 7 chain=A or chain=B render as Spline color by Chain
Background t_box size 700x700
time:72:46.08 megapov 10.25