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How do you select amino acids in jmol?

How do you select amino acids in jmol?

To select and display only the atoms of the sidechain of a specific amino acid, you want to use the select sidechain command followed by the amino acid name/number and end with the and (sidechain or alpha) text.

How do I select helix in jmol?

You can use the or Boolean Operator to select all the amino acids that are either part of alpha helices or the atoms that are part of the backbone. The phrase ‘select helix or backbone’ means ‘select all atoms that are either a helix or in the backbone (or both)’.

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.

Are the disulfide bonds an example of primary secondary or tertiary structural elements?

The overall three-dimensional structure of a polypeptide is called its tertiary structure. Disulfide bonds, covalent linkages between the sulfur-containing side chains of cysteines, are much stronger than the other types of bonds that contribute to tertiary structure.

How do you cite jmol?

How to cite Jmol. Remember to always use uppercase ‘J’, lowercase ‘mol’ (explanation). If you prefer, a list of articles that describe Jmol can be found in the Jmol Literature section of the Jmol Wiki.

How do I use jmol commands?

Try some of these commonly useful commands:

  1. “spin on” will cause the molecule to start spinning.
  2. “spin off” will stop the molecule from spinning.
  3. “moveto 0 {0 0 0} 0” will return to the default view.
  4. “select carbon” will select the carbon atoms in the file.
  5. “select hydrogen” will select the hydrogen atoms in the file.

How do I use Jmol commands?

How do I use Jmol console?

To open the console, right click anywhere in the black Jmol window and select “Console” from the menu that appears. You will want to arrange both windows so that they do not overlap, as they will be used at the same time. Your display should look similar to the image below.

Does amino acid substitution affect secondary structure?

D-Amino acid substitutions at the termini reduced the inhibition of the activity by heat-inactivated serum, which indicated that local change of chirality or change of secondary structure induced by D-amino acid substitutions might affect the interactions between the peptide and certain components in the serum.

What is an example of a secondary protein structure?

A secondary structure of a protein pertains to the folding of a polypeptide chain, resulting in an alpha helix, beta sheet or a random coil structure. Another example of a secondary structure is that of a nucleic acid such as the clover leaf structure of tRNA.

What does jmol stand for?


Acronym Definition
JMOL Judgment as a Matter of Law
JMOL Java Molecule (science software)