Draw lines connecting pair of atoms in PyMOL
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24 months ago
becko • 0

I have several pair of atoms and I wish to draw some lines between them PyMOL. The resulting image should be something like this:

enter image description here

Note that some lines are of a color and other lines are of a different color.

How can I achieve this kind of graphic in PyMOL (or any similar software)?

pymol • 2.5k views
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See the following post. It looks helpful.

Draw Bonds In Pymol And Color Them

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Thanks. How can I show the bonds I just created in the cartoon representation? They only appear to show in the liner representation of the molecule.

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Search this site

https://sourceforge.net/p/pymol/mailman/message/28460905/

and finally you will find the following post:

From: Thomas Holder <speleo3@us...&gt; -="" 2011-11-28="" 14:35:14<="" p="">

<> most trivial manner:

as cartoon show sticks, resn LEU+ILE+VAL set cartoon_side_chain_helper

and eventually something like this:

show spheres, resn LEU+ILE+VAL and not name N+O+C set sphere_transparency, 0.5

They are talking about hydrogen bonds, try to change the script accordingly.

Or study this short pymol-guide from link below:

http://bio3d.uib.no/pdfs/pymol.pdf

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