Trimming overlapping parts of a model



Remove parts of a model that overlap with another model. Useful if you have a good model for part of the your structure and you want to add in only the new parts from another model. This can be the case if you have a good AlphaFold2 model for most of your structure and a possibly overlapping model from another source.

How trim_overlapping works:

The trim_overlapping tool identifies all the residues in your model that have a CA (or P for nucleic acids) atom close to one in the model to avoid. The cutoff distance is typically 3 A for proteins and is adjustable. If the remaining residues lead to short segments, those segments are removed too. The shortest segment to keep is also adjustable.


Standard run of trim_overlapping:

Running trim_overlapping is easy. From the command-line you can type:

phenix.trim_overlapping my_model.pdb model_to_avoid.pdb

This will trim my_model.pdb to avoid model_to_avoid and write out my_model_trimmed.pdb

Possible Problems

Specific limitations and problems:


Additional information

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