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Similarity restraint: command line arguments

Appendix C1: Similarity restraints: command line arguments

Copyright © 2008 Global Phasing Ltd.
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Command line options overview

It is our intention that it should be easy for the user to apply LSSR similarity restraints. Accordingly command line options are provided for the most common applications. For expert users and sophisticated treatments .Gelly cards can be used. The process of switching from the automated options to a .Gelly card treatment is described below. The .Gelly cards themselves are described in the next appendix.

Automated setup of LSSR for NCS
command line option -autoncs

The -autoncs command line option will attempt to identify NCS within a structure and apply LSSR similarity restraints on positions. The -autoncs command line option can be used on the autoBUSTER command line or the gelly_refine command line,

The identification compares all pairs of chains within in a structure. For each pair it will assess the proportion of residues that has the same residue number and residue type (e.g., "ALA"). If this is above 80% then NOTE BUSTER type cards are written to activate LSSR restraints for the NCS identified. Note that water molecules are ignored by -autoncs. If no NCS is identified the -autoncs will report this and the run will continue.

Note that no restraint is placed on the temperature factors by the -autoncs option. If you wish to place harmonic restraints on temperature factors then this can be done by using the NOTE BUSTER_SIM_RESTRAIN_B .Gelly card. The process of switching from the automated options to a .Gelly card treatment is described below.

A practical example demonstrating the use of the -autoncs can be found in the 002 run of the basic NCS setup example found at the Global Phasing BUSTER Wiki.

autoncs and pruning, the -autoncs_noprune option

LSSR restraints remove much of the need to "prune out" parts of the structure that are NCS violators. This is because markedly distinct parts of the structure will result in different interatomic contact distances (so LSSR restraints will plateau). A problem arises where there are distinct but rather similar side chain conformations in different NCS copies. Here LSSR restraints will work hard to pull the conformations together. The -autoncs procedure includes a simple routine designed to identify such regions and automatically prune them from the LSSR restraints applied. The procedure is conservative taking the attitude "if in doubt prune it out". It will therefore remove some parts of the structure that could happily be left in NCS restraints. It is also not perfect and you may need to manually adjust the pruning, as described below.

If you want the automated NCS but do want the automated pruning option to used then use the -autoncs_noprune option rather than the -autoncs option. This can be a good idea at the start of a refinement where it can be expected that minor differences between NCS copies are yet to be of importance. The basic NCS setup example found at the Global Phasing BUSTER Wiki. shows how the -autoncs_noprune option can be usefully used (003) following on from an initial run with -autoncs_noprune. The pruning is shown to result in both a slight improvement in Rfree as well as getting rid of some difference map features caused by LSSR pulling together residues that are conformationally close but distinct in the different NCS copies.

autoncs* setting the weight with -autoncs_weight value

Automated LSSR setup to an external target pdb structure with -target filename.pdb

Setting the weight for automated target restraints with -target_weight value

Swapping equivalent atoms to improve NCS and/or target restraints with the -sim_swap_equiv or -sim_swap_equiv_plus options

Consider the side chain of a PHE residue:
        /       \
  -CB-CG        CZ
        \       /
it is common that two different NCS copies can be very similar other than atoms CD1 and CE1 match CD2 and CE2 and vice versa. The -sim_swap_equiv option works through the residues in the molecule checking whether the NCS (and/or target) restraint function is improved by swapping the coordinates, temperature factors and occupancies of relevant pairs of atoms. The check is done at the beginning of every big cycle and details of any residues swapped are written to the relevant LIST.html file. The use of this procedure will mean that IUPAB naming conventions for sidechains are likely to be broken. It is intended to address this in a future release.

The -sim_swap_equiv_plus option extends the swapping to residues that are quasi-symmetric such as ASN, GLN and HIS. Using this option may well disrupt hydrogen bonding patterns and it is advised to check its result. The option is dumb - if a residue has good hydrogen bonding in one copy but bad in the other it is equally likely the good will be swapped to the bad!

In general, for a given refinement the procedure needs only be applied once and should then not be used (it is slow and could disrupt sensible hydrogen bonding patterns).

The basic NCS setup example found at the Global Phasing BUSTER Wiki shows how the -sim_swap_equiv_plus option swaps 65 residues to improve NCS. This results in improved Rfree, Rfree-Rwork gap and geometry scores compared to leaving equivalent atoms to remain different.

Note that -sim_swap_equiv and -sim_swap_equiv_plus procedures will work both for LSSR restraints, superposition-based (RMSD) and/or temperature factor restraints. The restraints can be produced by command line options or in a .Gelly type file.

Manual adjustment of LSSR restraint conditions starting from the automated options

Page Author: Oliver S. Smart
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Last modification: 16.02.11