question about FFT map coefficients
Hello All, A quick question about the "FFT map coefficients" utility in the GUI: 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? If not, I can always change the sign of negative Fs and add 180 to the corresponding model phases, but I was hoping I could avoid this. Thanks in advance for the help! Mike P.S. I do know there is an Fo-Fo map option in phenix, but the origin of my map coefficients is more complicated than simply Fo-Fo, so I cannot use this option. -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles [email protected]
On Thu, Mar 28, 2013 at 3:28 PM, Michael Thompson
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. -Nat
Hi Mike, I guess all "FFT map coefficients" tool does is actually encoded in its name: Fourier transform map coefficients into actual map (3D function computed on a grid). So if you have what you want in input MTZ file then you should have what you want in output map file (in Xplor or CCP4 format). Pavel On 3/28/13 3:28 PM, Michael Thompson wrote:
Hello All,
A quick question about the "FFT map coefficients" utility in the GUI:
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? If not, I can always change the sign of negative Fs and add 180 to the corresponding model phases, but I was hoping I could avoid this.
Thanks in advance for the help!
Mike
P.S. I do know there is an Fo-Fo map option in phenix, but the origin of my map coefficients is more complicated than simply Fo-Fo, so I cannot use this option.
participants (3)
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Michael Thompson -
Nathaniel Echols -
Pavel Afonine