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Introduction to gelly

gelly Documentation : Introduction

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What is gelly?

This manual

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Using gelly within autoBUSTER

The gelly refinement module is automatically run with the autoBUSTER refine command provided refinement has been requested. The autoBUSTER command line options -Gelly and/or -RB can be used to provide files containing user specified .Gelly cards. Gelly cards all start with NOTE BUSTER and are used primarily to control restraint setup and parameter selection. gelly also has some command line options.

Doing geometry-only regularisation with gelly_refine script

The recommended way to run standalone gelly is by using the wrapper script gelly_refine supplied with autoBUSTER. Separate gelly_refine documentation is available. To see the main options for this type
gelly_refine -h
gelly_refine takes PDB files as an input, and automatically prepares the .seq, .cor, .tnt files needed to run gelly. As an example, for a simple run from the structure new_test.pdb
gelly_refine -p new_test.pdb -d test_dir -o test_dir/gelly_refine_out.pdb
This will run a geometry-only optimisation of the structure and write results to the directory test_dir. A geometry report for the initial and final structures will be produced together with a summary of the optimisation.

If you want to control the geometry function and/or parameter selection in gelly_refine use the -l <filename> option. This can be used to introduce a file of Gelly cards. For example if you want to geometry regularise only part of a molecule that has been rebuilt before full refinement. then produce a file with appropriate NOTE BUSTER_CONSTANT XYZ ... cards and use this with the -l option.

gelly command line options

Page Author: Oliver S. Smart
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Last modification: 16.02.11