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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2 votes
1 answer

From a PDB file, how may I know which atoms have bonds between them?

Suppose I have a protein PDB file, and I want to know which atoms have bonds between them. How can this be done? Sometimes people suggest using the CONECT field for ...
2 votes
1 answer

Why do I see a deviation when I compare PDBs using TMalign?

I constructed a PDB file of main-chain from its CA-trace using pd2_ca2main app. I used TMalign to compute RMSD values from those ...
6 votes
2 answers

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.
4 votes
1 answer

Why is this source code giving incorrect RMSD value?

Aligning PDB structures with Biopython The following source code is obtained from the above link: ...
2 votes
1 answer

Why is my pdb looking so weird? [closed]

I have generated the following pdb file for a polymer: ...
2 votes
0 answers

How can I compute the performance of an application software?

I am working with protein PDB files. Application 'A' generated 3884 PDB files from the protein's CA-trace. Application 'B' did the same. So, I calculated the CRMSD values of each pair of files for ...
3 votes
0 answers

How to fix outliers in Ramachandran plot using Coot [closed]

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 ...
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. ...
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.