[3dem] pdb for near-atomic resolution EM maps

[Ariel Blocker]

Dear Petr,
> I think there is a major confusion about what is modeling and what are experimentally determined constrains. Rotamer libraries are derived from experimental data, just like the rest of geometrical parameters. Low resolution refinement and data interpretation for that matter heavily rely on rotamer libraries. I mentioned MD in my previous message as something that seriously dedicated people might want to try using the structure that has been deposited to PDB or elsewhere as a main chain for which side chains have just been recreated. I never suggested depositing MD simulated data to PDB.
Oh, I see, that’s absolutely fine then. ;)

> On the other hand, I am a little disturbed by your remark that you chose to deposit a structure that clearly does not agree with your experimental map. Shouldn't it be a C-alpha trace or something similarly less precise than a complete atomic model?
No, the model we deposited does fit the (very low resolution envelope of the) map well. But, obviously, common sense tells you that’s not even a half-decent a criterium to use to suggest that its C-alpha trace is even vaguely accurate.

Best,
Ariel.
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