Hi, I'm trying to make a fem amp using phenix-1.8.4-1496 using my refined structure and mtz with map coefficients as input: phenix.development.fem 3222_Glu_refine_78.mtz 3222_Glu_refine_78.pdb coot 0.7.0-1 fails to generate a map when fem.mtz is opened, either in auto or manual mode mtzdmp for fem.mtz gives: Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 NONE -37 35 0 100.00 -5.0 14.2 61.69 1.21 H H 2 NONE 0 101 0 100.00 38.0 38.0 61.69 1.21 H K 3 NONE 0 44 0 100.00 16.8 16.8 61.69 1.21 H L 4 NONE 0.0 1796.7 25825 84.81 84.67 84.67 31.87 1.21 F 2mFoDFc 5 NONE -180.0 180.0 25825 84.81 1.07 90.28 31.87 1.21 P PHI2mFoDFc 6 NONE 0.0 2750.2 0 100.00 144.76 144.76 61.69 1.21 F 2mFoDFc_FilSharp 7 NONE -180.0 180.0 0 100.00 1.26 90.34 61.69 1.21 P PHI2mFoDFc_FilSharp 8 NONE 0.2 24426.8 0 100.00 235.27 235.27 61.69 1.21 F KICK 9 NONE -180.0 180.0 0 100.00 0.02 89.63 61.69 1.21 P PHIKICK 10 NONE 0.2 9283.0 0 100.00 132.01 132.01 61.69 1.21 F FEM 11 NONE -180.0 180.0 0 100.00 0.23 90.34 61.69 1.21 P PHIFEM
Phenix fem-map is fine. The 'bug' was caused by coot burying the window for selecting columns for map synthesis under the graphics window, so it appeared that coot never recognized the file, while instead it was waiting for input. I love coot, but buried windows (in Mac OS X) can be tricky at times. --
Hi Mark, just a quick remark: I made a number of improvements to FEM procedure recently, so it's best to use the latest version of Phenix (from your previous email I figure you used a slightly older version). All the best, Pavel On 10/23/13 10:43 AM, Dr. Mark Mayer wrote:
Phenix fem-map is fine.
The 'bug' was caused by coot burying the window for selecting columns for map synthesis under the graphics window, so it appeared that coot never recognized the file, while instead it was waiting for input. I love coot, but buried windows (in Mac OS X) can be tricky at times.
participants (3)
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Dr. Mark Mayer
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nih\mayerm
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Pavel Afonine