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.

The input for the carbohydrates can be either a string on the command-line or a file name containing the allowable formats.

• 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.

Optional inputs include:

• 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...