Fixing register errors in a model with fix_insertions_deletions



The routine fix_insertions_deletions is a tool for fixing register errors in a model by comparing the density at side-chain positions to a sequence file.


Normally you will access the functionality of fix_insertions_deletions by running the Phenix map_to_model tool in the Phenix GUI. However you can run it directly as well (there is no GUI for fix_insertions_deletions).

How fix_insertions_deletions works:

The fix_insertions_deletions tool examines the density in the supplied map at the position of each side chain in the supplied model and creates a table of side-chain probabilities corresponding to each segment in the model.

These side-chain probabilities are used to generate a map-based sequence for the model and map. This map-based sequence is then compared to the actual sequence to identify positions where the sequence register is likely to be incorrect, and what changes in register are needed to fix it.

Each place a register shift is needed is used as a target for main-chain rebuilding. During rebuilding the specified insertion or deletion is enforced so that only models with the desired changes are obtained (if possible).

Additional rebuilding of the worst-fitting regions is also carried out.

Using fix_insertions_deletions:

The tool fix_insertions_deletions is usually run automatically as part of trace_and_build. However you can run it yourself to try and fix up a model.

Input map file: The map file should cover the model you supply.

Resolution: Specify the resolution of your map (usually the resolution defined by your half-dataset Fourier shell correlation

Model: Supply a model that you want to fix. Only the main-chain will matter.

Sequence: Supply a sequence file that covers at least the part of the model that is supplied


Standard run of fix_insertions_deletions:

You can use fix_insertions_deletions to fix register shifts in a model based on a cryo-EM map:

phenix.fix_insertions_deletions my_map.mrc resolution=3 my_model.pdb seq.dat

Possible Problems

Specific limitations and problems:


Additional information

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