Basic examples

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Changing Display Format

load ftp 1smd Load the structure file (click here to see the detail of "load" command).
select all Select the whole of the molecule (in fact, this procedure is not necessary, because all the atoms are already selected just after the file is loaded). To see the detail of "select" command, click here.
[Display]-[Backbone] Change the format to backbone expression.
Amylase from PDB:1smd in backbone expression
select 91-103 Select the residues from 91 to 103 of each chain (actually this entry has only one chain).
color red Change the color of the selected atoms to red (click here to see the detail of "color" command).
backbone 1.0 Change the backbone thickness (radius) of the selected atoms to 1.0 angstrom (click here to see the detail of "backbone" command).
Amylase from PDB:1smd in backbone expression with the region between 91 and 103 residues are emphasized.
  • Similar example in Japanese is available from here.

Moving the Rotation Center

load ftp 1zcd Load the structure file (click here to see the detail of "load" command).
Na(+)/H(+) antiporter 1 from PDB:1zcd.
select all Select the whole of the molecule (in fact, this procedure is not necessary, because all the atoms are already selected just after the file is loaded). To see the detail of "select" command, click here.
wireframe off Turn off the wireframe expression of the selected region (click here to see the detail of "wireframe" command).
Na(+)/H(+) antiporter 1 from PDB:1zcd. All display of the atoms are turned off.
select *:a Select all the atoms in chain a.
[Display]-[Cartoon] Change the format to cartoon expression.
Na(+)/H(+) antiporter 1 from PDB:1zcd. Only the chain A is displayed.
* In this state, it is not convenient to move the molecule, because the rotation axis doesn't exist at the center of displayed region. To solve it, the following command should be execute.
center *:a Move the rotation axis and the position of molecule to the center of display area (click here to see the detail of "center" command).
Na(+)/H(+) antiporter 1 from PDB:1zcd. Only the chain A is displayed. Moved to the center.
  • Similar example in Japanese is available from here.

Selecting Atom

load ftp 1mbn Load the structure file (click here to see the detail of "load" command).
Myoglobin from PDB:1mbn.
select hem Select the heme group of this molecule (click here to see the detail of "select" command).
[Display]-[Ball&Stick] Change the format to ball and stick expression.
Myoglobin from PDB:1mbn.The expression of the heme group was changed to ball and stick.
select iron Select the iron atom. The same procedure can be execute by the command "select elemno=26".
cpk The expression of the selected atom turned to spacefill expression (click here to see the detail of "cpk" command equal to "spacefill" command).
The expression of the heme group was changed to the ball and stick, and that of iron atom was changed to the spacefill.
select atomno=1217 Select the atom with its atom number is 1217 (oxygen).
Myoglobin from PDB:1mbn.The expression of the heme group was changed to the ball and stick, and those of iron atom and the neighbor oxygen atom were changed to the spacefill.
  • The atom number is included in the value of the id attribute of "PDBx:atom_siteCategory/PDBx:atom_site" element in each PDBML file.
  • Similar example in Japanese is available from here.
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