Questions tagged [pdb]
For questions related to the Protein Data Bank file format, e.g. information included, converting to/from this format.
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 ...
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 ...
Why is this source code giving incorrect RMSD value?
Aligning PDB structures with Biopython The following source code is obtained from the above link: ...
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 ...
Why is my pdb looking so weird? [closed]
I have generated the following pdb file for a polymer: ...
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.
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 ...
Gromacs generate charges for a .pdb file
I have a .pdb file containing water molecules. ...
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.