Create xyz-axis for PyMol

Summary: When show protein unit cell in PyMol, I want to show xyz axis, but PyMol doesn’t have this option. Here is a solution.

Contents:

• Step 1: Create xyz axis file
• Step 2: Edit the xyz_move.pdb file in PyMol
• Step 3: Show xyz-axis in PyMol

Check this blog on github

*The code and file are available here

fig 1: Preview of protein unit cell

Step 1: Create xyz axis file

The following MATLAB code is used to create xyz axis.

%set origin point to (-10,-10,-10)
x=1:50;
a_axis = zeros(length(x),3);
a_axis(:,1) = x';
b_axis = zeros(length(x),3);
b_axis(:,2) = x';
c_axis = zeros(length(x),3);
c_axis(:,3) = x';
abc_axis=[a_axis; b_axis; c_axis];
abc_axis=abc_axis-10;

fl_ID_name="xyz_move.pdb";
fl_ID=fopen(fl_ID_name,'w');
for m=1:length(abc_axis)
    x=abc_axis(m,1);
    y=abc_axis(m,2);
    z=abc_axis(m,3);
    fprintf(fl_ID,'%4s%7d%3s                %8.3f%8.3f%8.3f%6.2f%6.2f\n',... %%%16 spaces
                'ATOM',m,'  H',x,y,z,1.0,0.05);
end

The axis’ origin point is set to (-10, -10, -10) so that it won’t overlap with the unit cell origin. Each axis has 50 points.

Step 2: Edit the xyz_move.pdb file in PyMol

Open the xyz_move.pdb file in PyMol(fig 2):

fig 2: Show xyz_move.pdb in PyMol

Select xyz axis

Type following command one by one in the command input area:

select a, id 1-50 # x-axis

select b, id 51-100 # y-axis

select c, id 101-150 #z-axis

*Learn PyMol command at here

Now it looks like this:

fig 3: Select xyz axis in PyMol

Color xyz axis

Look at the red block in fig 4, for the selected

• a, click C, then choose red -> red
• b, click C, then choose green -> greem
• c, click C, then choose blue -> blue

fig 4: Color xyz axis

Now xyz axis has been colored with red, green, blue respectively.

Label xyz

Right click the last atom at x-axis, menu -> edit label (upper figure in fig 5). In the middle figure, at right lower corner, choose label size: 36, at left upper corner, input capital x, enter.

Same for the y, z axis.

The result is in the lower figure.

fig 5: Label xyz axis

Click File -> Save Session, named xyz_move_colored.pse.

Step 3: Show xyz-axis in PyMol

Open the saved session, choose “Merge with current session”, now you will see fig 6.

fig 6: Show xyz axis in PyMol