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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.

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  • $\begingroup$ Is it a PDB (Protein Data Bank) file with macromolecular structure? $\endgroup$ – marcin Feb 15 '18 at 18:06
  • $\begingroup$ @marcin, yes it is $\endgroup$ – wanlei Feb 15 '18 at 21:52
  • $\begingroup$ "the raw PDB file (without minimization)" - this is not clear to me $\endgroup$ – marcin Feb 15 '18 at 23:28
  • $\begingroup$ 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. $\endgroup$ – wanlei Feb 16 '18 at 1:22
  • $\begingroup$ No, they usually don't. Perhaps you think about restraints that are used during the refinement. $\endgroup$ – marcin Feb 16 '18 at 13:09
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The process of making structural models of macromolecules (the content of PDB files) is called model building, rather than generating, because it normally involves tedious manual building of the model in a graphical program such as Coot. A few programs can do automatic model building, but then the structure needs to be finished manually. Maybe this will change in the future. All these programs have rather steep learning curve, so it's probably not what you are looking for.

The next problem is that you plan to start from an electron density map. Assuming that the experimental method was crystallography, not Cryo-EM, the electron density map is derived from both reflection data and the model (and at the same time the model is built into the map, iteratively). So for the purpose of re-building or validation people generally use reflection data, not the map.

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