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| Line 511: |
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| to the phenix.refine command line results in the log file containing memory usage throughout the run. Look for the max memory intake in the last record (towards the end of log file). This will give you an idea about how much memory you may need. | | to the phenix.refine command line results in the log file containing memory usage throughout the run. Look for the max memory intake in the last record (towards the end of log file). This will give you an idea about how much memory you may need. |
| It might well be that this also works for the other phenix tools. | | It might well be that this also works for the other phenix tools. |
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| == Refinement with mmtbx.lockit ==
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| From RWGK's posting to [http://www.phenix-online.org/mailman/listinfo/phenixbb phenixbb] on Nov 14, 2010:
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| We have a tool for quick real-space refinement that's geared towards making the
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| geometry ideal in the end. I'm not sure it is useful in your situation, but may
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| be worth a try. It works like this:
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|
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| mmtbx.lockit your.pdb your_refine_001_map_coeffs.mtz \
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| map.coeff_labels.f=2FOFCWT,PH2FOFCWT coordinate_refinement.run=True \
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| atom_selection='resname LIG'
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|
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| It works in two stages. First it attempts to maximize the real-space weight
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| allowing for a significant (but not totally unreasonable) distortion of the
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| geometry. This is meant to move the ligand into the density. In the second stage
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| it scales down the "best" real-space weight and runs a number of real-space
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| refinements until the selected atoms do not move anymore. The expected result is
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| nearly ideal geometry.
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| The procedure is usually very quick. If it turns out to be useful we could
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| integrate it into phenix.refine, to be run after reciprocal-space refinement.
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|
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| The mmtbx.lockit command is not as user-friendly as phenix.refine. It only works
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| with mtz files, you have to manually specify the mtz labels, and the error
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| messages may be unhelpful. Also be sure there is a valid CRYST1 card in your pdb
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| file.
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| == Maps == | | == Maps == |