I am trying to plot the following points in VMD. It is plotting as points. However, It is not connecting the points from A to B to C to D to E to F to H by a line. How do I do it? If not in VMD, Is there any other software where I can do this.
This is what I get if I open your file in PyMOL. Of course, I have to specify "hide spheres" and "show lines", as the points are fare too close together to be actual atoms. Even in stick representation, they overlap too much to show any details.
As all "interatomic" distances in this set of coordinates are well within the bond recognition distance cutoff, you would have to use the "unbond" command to remove the lines you do not want (https://pymolwiki.org/index.php/Unbond)
I found Jmol (http://jmol.sourceforge.net/) interesting to play around with this coordinate file. You try this as well. I also tried to visualize your file and it looks like as shown in the attached image. There is Model Kit tool in the tool that I have encircled in the image which you can use to drag and adjust overlapping atoms.
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