Sails - Software for the Automated Identification of Linked Sugars

Overview

Sails is a software package for automatic addition of glycans to protein models obtained through X-ray crystallography. Sails uses the output of GlycoFind to be able to build glycans quickly and accurately.

Authors

Jordan Dialpuri - York Structural Biology Laboratory, University of York

Installation and setup

Prerequisites

You must have

• Clipper
• MMDB2

installed, which come included in the CCP4. To ensure they are in your path, you must source the appropriate script. To do this run:

source /opt/xtal/ccp4-X.X/bin/ccp4.setup-sh 

where X.X is your CCP4 version.

Usage

To run the executable run:

./sails <PARAMS>

The available parameters are

-pdbin <filename>
-mtzin <filename>        
-predin <filename>
-colin-fo <colpath>
-colin-hl <colpath> or -colin-phifom <colpath>
-colin-fc <colpath>
-colin-free <colpath>
-resolution <float>

Description

pdbin - a model to add sugars to

mtzin - the input reflections data from the experiment e.g. 5fji.mtz

predin - the predicted map from GlycoFind

colin-fo - column headings for F_obs e.g. FP, SIGFP

coln-hl - column headings for Hendrickson-Lattman coefficients (ABCD) e.g. sfcalc.A, sfcalc.B, sfcalc.C, sfcalc.D

colin-fc - column headings for F_calc e.g FWT, PHWT

colin-free - column heading for Free R Flag

resolution - the resolution cutoff to use

Development

Apple Silicon

To build for Apple Silicon run

./build.sh

Other

To build for other platformrs run

make -j