[phenixbb] question about FFT map coefficients

Michael Thompson miket at chem.ucla.edu
Fri Mar 29 10:31:21 PDT 2013

Hi Nat,

The FFT didn't work out, but I'm not sure if it's due to negative Fs. When I set up the FFT map coefficients utility with my mtz file, after picking my input I get a warning that "The reflections file does not appear to contain any suitable map coefficients." Then if I try to run it anyway I get the error message "There are no map coefficients in this MTZ file."

An mtz dump confirms that I have columns FP and SIGFP. Additional info: these Fs were generated using a python script that I wrote, and there are not meaningful values for SIGFP. My script simply wrote out 0.000 to the SIGFP column for each reflection essentially as a place holder. I thought that maybe 0 was not a valid entry for SIGFP so I changed it to 0.001 so there would be some value there, but I get all the same errors. Could this be the problem?

Any suggestions?

Thanks for the help. Sorry to bug you.


----- Original Message -----
From: "Nathaniel Echols" <nechols at lbl.gov>
To: "PHENIX user mailing list" <phenixbb at phenix-online.org>
Sent: Thursday, March 28, 2013 3:42:31 PM GMT -08:00 US/Canada Pacific
Subject: Re: [phenixbb] question about FFT map coefficients

On Thu, Mar 28, 2013 at 3:28 PM, Michael Thompson <miket at chem.ucla.edu> wrote:
> I have an mtz file with map coefficients that are essentially Fo-Fo for two data sets. I would like to generate a map using these coefficients, but because the subtraction of Fs has already been done, there are some values of FP that are negative. Is "FFT map coefficients" able to handle negative values for FP?

My guess would be that the answer is yes, because internally the
amplitudes and phases for map calculation are combined to form a
single array of complex numbers, and this effectively converts the
amplitudes to be all-positive.  Also, if this were not the case, the
isomorphous or anomalous difference maps would never work.  But I
haven't actually tried what you're wanting to do with real data - if
the result isn't what you expect, let us know.

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Michael C. Thompson

Graduate Student

Biochemistry & Molecular Biology Division

Department of Chemistry & Biochemistry

University of California, Los Angeles

miket at chem.ucla.edu

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