How do I change the atom color in Jmol?
You can change the default either to the Rasmol “CPK” standard or the Jmol standard, or you can customize any specific element’s color. You can explicitly assign atom colors to elements using JavaScript standard color names, octal equivalents, or RGB triples.
How to change display in Jmol?
The Command Line Commands to alter the Jmol display are entered in the console. Click in the white area of the Jmol Console to enter commands. This area, highlighted by a magenta dollar sign ($), is where text commands are entered. After typing a command and hitting enter, the command will execute.
What are the colors of atoms?
The colours of the various atoms within the molecules follow the standard CPK rules:
- Hydrogen = White.
- Oxygen = Red.
- Chlorine = Green.
- Nitrogen = Blue.
- Carbon = Grey.
- Sulphur = Yellow.
- Phosphorus = Orange.
- Other = Varies – mostly Dark Red/Pink/Maroon.
How do you pick a chain in Jmol?
Select Chain With select :, followed by the letter of the chain you would like to select, only the chain you select will be affected by future commands. Note: The Top 7 protein is a protein with only a single chain, so all atoms are colored red with the commands used above. Hemoglobin based on the file 1a3n.
How do I use JSmol?
JSmol Example The structure below is rendered using JSmol, if you click and hold down on the mouse you should be able to rotate it, alt-click rotates in the z-plane, shift-click is zoom (or you can use the scroll wheel on your mouse).
How do I rotate in Jmol?
You can try this in an open Jmol application or by clicking the link in figure 2 to convert it to a live Jmol display. To have spinning about axes other than Y select the rate (degrees per step) for rotation about the X or Z axis. Use the pop-up menu (Right mouse button > Spin > Set X (Y or Z) Rate > XX).
How do I use Jmol commands?
Try some of these commonly useful commands:
- “spin on” will cause the molecule to start spinning.
- “spin off” will stop the molecule from spinning.
- “moveto 0 {0 0 0} 0” will return to the default view.
- “select carbon” will select the carbon atoms in the file.
- “select hydrogen” will select the hydrogen atoms in the file.
What molecule is black?
Common CPK Coloring Chart
| Element | Color |
|---|---|
| carbon | black |
| nitrogen | dark blue |
| oxygen | red |
| fluorine and chlorine | green |
Is oxygen red or blue?
Hemoglobin bound to oxygen absorbs blue-green light, which means that it reflects red-orange light into our eyes, appearing red. That’s why blood turns bright cherry red when oxygen binds to its iron. Without oxygen connected, blood is a darker red color.
How do you identify amino acids in jmol?
If you do not know the amino acid number, chain letter, amino acid type, or atom number of the item you want to select, you can click on the structure in the Display Window. Jmol will provide information on the Console Window regarding the atom you clicked on.
How do you select hydrogen bonds in jmol?
To remove just a single hydrogen bond, select only the two amino acids that the hydrogen bond connects and then use the hbonds off command. When Jmol calculates hydrogen bonds, it occasionally inserts a hydrogen bond between two amino acids on the same strand, with a single amino acid between the two.
How do I download Jsmol?
Downloading Jmol You need to have Java on your computer to run the desktop version of Jmol. Most computers will already have Java installed, but if you do not, you can download it for free from https://java.com/en/download/.