The error message in coot says: Failed to find any suitable F/phi columns in the MTZ file. On Mon, Feb 14, 2011 at 6:29 PM, Jason wrote:

Hi,

Let me clarify my problem again.

I used both command line and GUI of phenix.maps to generate a map file: xxx_map_coeffs.mtz. This file (both command line way and the GUI way) can not be loaded into coot (version 0.6.1). However, when using GUI, there is a link to coot (an icon says display in coot). If I press this icon, the map can be displayed in coot. I am running under MAC OS X version 10.6.3.

On Mon, Feb 14, 2011 at 6:00 PM, Jason wrote:

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Hi everyone,

I have noticed that the coefficient mtz file generated by phenix.maps can't not be loaded to coot (it can be read through the link in the GUI version once after process). I am using 1.7 version. Any suggestions?

-- ====================== Jason Structural Biology Department University of Pittsburgh ======================

-- ====================== Jason Structural Biology Department University of Pittsburgh ======================

-- ====================== Jason Structural Biology Department University of Pittsburgh ======================

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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

On Mon, Feb 14, 2011 at 3:31 PM, Jason wrote: 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 2FOFCWT_filled/PH2FOFCWT_filled. Pavel.