[phenixbb] Generating electron density from protein coordinate (PDB)

Pavel Afonine pafonine at lbl.gov
Thu Mar 19 22:11:10 PDT 2020

Hi Simon,

> I tried phoenix.model_map and it successfully generates ccp4 and xplor 
> files. 

note, this generates a model-calculated exact map (infinite resolution). 
I'm not sure this is what you want, thinking of practical applications. 
You can always FT this map to get an image of it at particular 
resolution, but this is a separate step. Just making sure you are aware 
of all of this.

> However, I fail to understand the xplor file format for further 
> analysis. Is there any suggested documentation on xplor (ccp4) format? 

While X-plor is old format (yet much easier to understand and deal with 
at low-level than ccp4), ccp4 is pretty much the standard these days 
with most software being able to deal with it. So I'd say some web 
search should get you up to speed!

> Visualization on pymol also suggests that my electron density was 
> truncated by the box boundary. Is there any way to first centralize 
> the box at the core of the protein, then create a box with a defined 
> (sub)region of the PDB?

Perhaps you want to calculate the map in the entire unit cell and then 
choose how to crop it for your convenience.

Does this answer your questions? Do you still have more? Please feel 
free to let us know and we will follow up!


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