Questions tagged [pdb]

For questions related to the Protein Data Bank file format, e.g. information included, converting to/from this format.

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How to fix outliers in Ramachandran plot using Coot

I have the following Ramachandran plot generated by Coot: Notice that it has high outliers content (red dots). I want to manually drag those red dots into some part of the region. Eventually, I ...
  • 1,612
2 votes
0 answers

Why is my pdb looking so weird?

I have generated the following pdb file for a polymer: ...
  • 3,957
6 votes
1 answer

How to show orientation axis in Pymol

Is there a way to show the orientation axis in Pymol? It's something like this in VMD. I much prefer Pymol rendering.
  • 1,612
8 votes
2 answers

Limits of periodic box from pdb

I have a pdb file of some solvent molecules in a box of 20 Angstroms I have built using Tinker. I have opened the file with Chimera, Molden, Pymol and Avogadro... but I would like to see, and maybe ...
7 votes
1 answer

Gromacs generate charges for a .pdb file

I have a .pdb file containing water molecules. ...
  • 1,083
6 votes
3 answers

How to extract specific frames/model from a multi model pdb file?

I have a multi model pdb file and would like to extract the last frame or any other frame from it.
  • 1,311