[phenixbb] Can PHENIX write the peak list to a PDB file?

Pavel Afonine PAfonine at lbl.gov
Wed Sep 23 12:30:33 PDT 2009

Hi Joe,

> PHENIX has an option to find positive and negative peaks, but only lists 
> them in the log file along with the residue they are closest to. 

I have done it this way having the following in mind:

- you load you refined model and maps in your favorite graphics program, 
Coot for example;
- you take that +/- peaks list;
- and you go residue-by-residue and check the flagged peaks.

> Is it 
> possible to write out the actual peak coordinates, such as to a PDB file?

It's possible of course, but I have a couple of questions:

- why to do this?
- what do I put as atom name, residue name, occupancy, B-factor, atom 
chemical type ?

Thanks again for your feedback!

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