# Generating PDB file from electron density without force field minimization

Is there a step-by-step tutorial on how to generate a PDB file from an electron density file (*.ccp4)?

For my current project, I am trying to take some statistics of some PDB files. However, I do not think that the empirical energy function (MM) implemented in x-plorer could accurately reproduce experimental or QM data. As a result, I would like to use x-plorer to generate the raw PDB file myself (without minimization), but since I have never done this before, I was wondering if somebody could provide me some guidance on how this could be done.

• Is it a PDB (Protein Data Bank) file with macromolecular structure? – marcin Feb 15 '18 at 18:06
• @marcin, yes it is – Astronomer Feb 15 '18 at 21:52
• "the raw PDB file (without minimization)" - this is not clear to me – marcin Feb 15 '18 at 23:28
• all PDB structures undergo force field minimization after the x-ray diffraction data is obtained. This is done for refinement purposes. However, force fields are far from perfect, and I was interested in the structures from the raw diffraction data. – Astronomer Feb 16 '18 at 1:22
• No, they usually don't. Perhaps you think about restraints that are used during the refinement. – marcin Feb 16 '18 at 13:09