[phenixbb] phenix.maps

Pavel Afonine pafonine at lbl.gov
Mon Feb 14 19:53:25 PST 2011

> On Mon, Feb 14, 2011 at 3:31 PM, Jason<phenix.upitt at gmail.com>  wrote:
>> The error message in coot says: Failed to find any suitable F/phi columns in
>> the MTZ file.
> Okay, I just confirmed the problem.  Coot only recognizes a limited
> set of MTZ labels as maps when using the "Auto Open MTZ" function, and
> there are multiple different conventions for output labels (and MTZ
> file structure) in Phenix, with the result that there are probably
> hundreds of lines of code in the GUI to deal with displaying map
> files.
> There are two separate problems in your case.  The GUI defines the
> default maps with PHI labels PHI2FOFCWT and PHIFOFCWT - Coot prefers
> just "PH" instead of "PHI" here.  I'm fixing that now, but for now you
> can edit the PHI labels to delete the "I".  The command-line version
> has a different convention: for a 2mFo-DFc map, the labels will be
> 2mFoDFc/P2mFoDFc, and so on.  Coot doesn't recognize these either, so
> you'll need to edit the parameter file here.  Alternately, in either
> case you can still use the "Open MTZ..." menu item in Coot to define
> the labels yourself.  Sorry for the confusion; I'll look into making
> all of the programs behave the same.

Personally, I always open maps in Coot using "Open MTZ, ...", since, as 
Nat mentioned, there are plenty of reading/writing map labels 
conventions and it's hard to know what will be read in and shown to you 
automatically. Although PHI2FOFCWT vs PH2FOFCWT, or 2mFoDFc/P2mFoDFc are 
probably obvious enough to pick up automatically if no other similar 
option is available.

> (Fortunately, it looks like
> phenix.refine's default map types use the appropriate labeling.)

Even here there is an inconsistency: what phenix.refine labels as 
2FOFCWT/PH2FOFCWT (only to satisfy Coot) phenix.maps would label as 


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