Question: Draw lines connecting pair of atoms in PyMOL
0
gravatar for becko
12 months ago by
becko0
becko0 wrote:

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 • 958 views
ADD COMMENTlink modified 12 months ago by natasha.sernova3.7k • written 12 months ago by becko0
1

See the following post. It looks helpful.

Draw Bonds In Pymol And Color Them

ADD REPLYlink written 12 months ago by natasha.sernova3.7k

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.

ADD REPLYlink modified 12 months ago • written 12 months ago by becko0

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

ADD REPLYlink modified 12 months ago • written 12 months ago by natasha.sernova3.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1772 users visited in the last hour