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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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 ...
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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 ...
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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 ...
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Why is this source code giving incorrect RMSD value?
Aligning PDB structures with Biopython
The following source code is obtained from the above link:
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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 ...
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Why is my pdb looking so weird? [closed]
I have generated the following pdb file for a polymer:
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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.
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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 ...
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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.
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