CarboLoad

Overview

Input files

Output files

References

Overview

CarboLoad will load carbohydrates into your model. It can be used in several modes. The first mode is designed to find all possible N-linking sites. phenix.carbo_load model.pdb will output a list of all ASN residues that are in the motif for N-linking to carbohydrates.

Input files

CarboLoad requires a number of inputs and also has some options, all of which are provided using the phil formalism. The list of required inputs:

• protein_pdb_file_name: this is a file containing the protein model of current interest into which the carbohydrates will be loaded. It is best to have a CRYST1 record in place.
• map_coeffs_file_name: this is a maps coefficients file output from a phenix.refine run.
• data_file_name: a data file. A maps coefficients file is saved for possible use in subsequent runs as it saves time.

• carbohydrate_file_name: this is a file containing chemical information about the carbohydrates.
  1. GlycoCT : This can be generated using the Carbohydrate Builder in REEL.
  2. Simplified Carbohydrate Line-Entry System (SCaLES) : The majority of carbohydrates linked to proteins a N-linked shorted polymers of high mannose. The add the first three units the parameters can be set to "NAG-NAG-MAN". More details are available here.

• output.file_name: Name of the output files.

Output files

By default, CarboLoad will generate a PDB file with the loaded carbohydrates and the linking files. These are no longer required by phenix.refine but are instructive.

References

GlycoCT...