March 2022 - phenixbb - phenix-online.org

Coot opening problem
by Afshan Begum 03 Mar '22

03 Mar '22

Hi Expert, I am refinening my strcuture on phenix , Could you kindly suggest me why after refinement in phenix (version i used 1.9-1692, Mac operation system) COOT does not open up by clicking on COOT button.Its seems open but only black screen (or blank window) come up without out any data, As previously always its open very smoothly , so now i have to open all files manually every time. Best Regards =============================== Afshan Begum

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Output MTZ file from Phenix Refine
by Mark Saper 02 Mar '22

02 Mar '22

Thanks to Tom the issue is resolved. If I examine the MTZ file with phenix.mtz.dump the angles are in degrees as they should be. For some reason CCP4 ViewHKL program shows them in radians although they are stored internally as degrees. > The output MTZ from Phenix refinement contains F-model and PHIF-model. I wanted to use the PHIF-model term in CCP4 but I discovered that PHIF-model in a Phenix mtz is in radians while CCP4 expects degrees. Why the discrepancy? > > -Mark _____________________ Mark A. Saper, Ph.D. Associate Professor Emeritus of Biological Chemistry University of Michigan Medical School saper(a)umich.edu | +1 734 276 6505 Powered by Mailbutler <https://www.mailbutler.io/?utm_source=watermark&utm_medium=email&utm_campai…>, the email extension that does it all

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Output MTZ file from Phenix Refine
by Mark Saper 02 Mar '22

02 Mar '22

The output MTZ from Phenix refinement contains F-model and PHIF-model. I wanted to use the PHIF-model term in CCP4 but I discovered that PHIF-model in a Phenix mtz is in radians while CCP4 expects degrees. Why the discrepancy? -Mark _____________________ Mark A. Saper, Ph.D. Associate Professor Emeritus of Biological Chemistry University of Michigan Medical School saper(a)umich.edu | +1 734 276 6505 Powered by Mailbutler <https://www.mailbutler.io/?utm_source=watermark&utm_medium=email&utm_campai…>, the email extension that does it all

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