Author(s)

• trim_overlapping: Tom Terwilliger

Purpose

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.

Examples

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:

Literature

Additional information

List of all available keywords

• job_title = None Job title in PHENIX GUI, not used on command line
• input_files
  • model = None Input PDB file to trim
  • model_selection = None If specified, only consider selected part of model
  • model_to_avoid = None Input PDB file to not overlap
  • model_to_avoid_selection = None If specified, only avoid selected part of model_to_avoid
• output_files
  • trimmed_model_prefix = None Output files with superposed models will begin with this prefix
• trim_overlapping
  • min_dist = 5 Remove residues within this distance of target model
  • minimum_fragment_length = 7 Minimum length of a segment after trimming (toss if shorter)
  • unique_chain_id = None Unique chain ID not present in models. Used internally
• control
  • write_files = True Write output files
• guiGUI-specific parameter required for output directory
  • output_dir = None