Visual fragment placement in MarvinSketch
Templates can be placed
visually in MarvinSketch. It means that
when you picked one up, you can immediately see it moving with the mouse
cursor.
Joining a template to a structure:
- Select a template (Cyclopentane in the example).
- Move it near the structure.
The attaching points are signed by circles.
- Click.
Joining a template while rotating it into the desired angle:
- Select another template (Naphtalene).
- Move it near the structure to attach in one point.
- Hold the mouse button down and start to rotate by moving the mouse.
- The other attaching point becomes visible (signed by circle) when the
template is almost in the desired angle.
- Release mouse button.
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Template placement in two different ways
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The same can also be done with selections.
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In Marvin, you can rotate a fragment that is attached to the molecule in a
single point, in such a way that the attachment point will be the rotation
center.
- Select atoms.
- Move the mouse pointer from the rotation center into a distance where
the rotation symbol appears.
- Press the mouse button and hold it down while rotating.
- The attaching point becomes visible when the
selection is almost in the desired angle.
- Release mouse button.
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How to rotate a part of the sketch.
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Notice that in the last step of all the examples, the templates were
automatically translated and rotated to fit exactly in the molecule. It is
natural but it may be a surprise if you are new only to Marvin and already know
other molecule sketcher applets.
The simplicity of fragment placement is a feature unique to MarvinSketch since
the beginnings.
