User:James D Watson/Using Jmol: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older editNewer edit →
No edit summary
No edit summary
Line 65: Line 65:
'''''Main | Style | Atoms | Off'''''<br/>
'''''Main | Style | Atoms | Off'''''<br/>
<br/>
<br/>
This leaves the remaining bound small molecules. Explore the structure some more to confirm the identity of these tightly bound molecules as the haem groups. <scene name='User:James_D_Watson/Using_Jmol/Haemoglobin_checkpoint2/1'>"Check Section"</scene>
This leaves the remaining bound small molecules. Explore the structure some more to confirm the identity of these tightly bound molecules as the haem groups (''Hint: Toggle off the spinning and click on the Jmol window. Moving your cursor over an atom should provide a pop-up window identifying that atom/residue'').<br/>
<scene name='User:James_D_Watson/Using_Jmol/Haemoglobin_checkpoint2/1'>"Check Section"</scene>
<br/>
<br/>
{{Clear}}
{{Clear}}


 
Now let's focus in on a haem group to see how it interacts with the protein. redisplay the pigment, this time as a "ball and stick" model, and also with the atoms colored by element.
What if you only want to see the protein, without the pigments?
 
Select | Hetero | Ligand
Render | Bonds | Off
 
The pigments (which are ligands of this protein) were displayed as bonds only, so turning off the bonds turned off the display of the pigments altogether.
 
Now let's redisplay the pigment, this time as a "ball and stick" model, and also with the atoms colored by element.


Select | Hetero | Ligand
Select | Hetero | Ligand
Retrieved from "https://proteopedia.org/User:James_D_Watson/Using_Jmol"