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Similarity restraint syntax

Appendix C2: Similarity restraint: .Gelly card specifications

Copyright © 2008 Global Phasing Ltd.
All rights reserved.


Contents


Overview

The use of NCS restraints in refinement can be complex. Because of this we have introduce LSSR similarity restraints and simple to use command line arguments to use these. These should cover many common applications. However, the automated setup methods may need manual tweaking. In addition users may want to use sophisticated treatments. This appendix describes the .Gelly cards allow the application of different kinds of restraints for both NCS and to target structures. See also, how to use .gelly cards in autoBUSTER.


Defining similarity groups for NCS with the NOTE BUSTER_SIM_DEFINE card

This card is used to define a "similarity group". The card syntax is:
NOTE BUSTER_SIM_DEFINE <Group_name> <Set_specifier> <Related_chain_list> ...
where:
<Group_name>: this is an arbitary user defined group name. It is usually best to make this informative. For instance in define an NCS relation between chain A and B a good group name would be "ncsAB", but if you wanted you could call it "Peter_Rabbit".
<Set_specifier>: This is used to define the template atoms for the NCS relation. The template must be from a single chain but can be all or any part of this. Set_specifier can either be (a) a buster set name - for instance 'Chain_D' or (b) a direct atom selection within curly brackets, for instance { D|*:CA } for just CA atoms in chain D. (Further explanation)
<Related_chain_list>: this is a list of chains whose atoms are to be restrained to the position of the corresponding atom in the template after superposition. Note that the template chain name must not be specified. If more than one related chain is given restraints are used between all pairs of chains but only for atoms whose equivalents are in the template. (The word 'null' should be used to specify the blank chain.)

Examples


Using LSSR restraints for a similarity group with NOTE BUSTER_SIM_RESTRAIN_LSSR card

Once a similarity group has been defined (with a NOTE BUSTER_SIM_DEFINE card) LSSR restraints can be activated for this group with a NOTE BUSTER_SIM_RESTRAIN_LSSR card. The theory of LSSR restraints is detailed elsewhere. The card syntax is:
NOTE BUSTER_SIM_RESTRAIN_LSSR <Group_name> [Weight]
where:
<Group_name>: this is a user defined similarity group name that has already defined with a NOTE BUSTER_SIM_DEFINE card or a NOTE BUSTER_SIM_RESTRAIN_JOINT card.
[Weight]: this is a optional weight. The weight must be a positive real number. If no weight is given the default weight of 1.0 is used.


Using RMSD based positional restraints for a similarity group with NOTE BUSTER_SIM_RESTRAIN_RMSD card

Once a similarity group has been defined (with a NOTE BUSTER_SIM_DEFINE card) superposition based RMSD restraints can be activated for this group with a NOTE BUSTER_SIM_RESTRAIN_RMSD card:
NOTE BUSTER_SIM_RESTRAIN_RMSD <Group_name> [sigma_XYZ]
where:
<Group_name>: this is a user defined group name that has already defined with a NOTE BUSTER_SIM_DEFINE card or a NOTE BUSTER_SIM_RESTRAIN_JOINT card.
[Sigma_XYZ]: is a optional positive real number specifying the sigma to be used on the restraint in Å. Each atom pair in the restraint will contribute separately with this sigma. If no Sigma_XYZ is specified then a sigma will be obtained from the "WEIGHT NCS" that is current. The TNT "WEIGHT NCS" value is normally set by the autoBUSTER parameter wncs. The default value for wncs is 50). Following the practice of the TNT ncs program Sigma_XYZ is set to 1/sqrt(wncs) (if not specified on the card). The default Sigma_XYZ is accordingly 0.14Å.

Using temperature factor restraints for a similarity group with NOTE BUSTER_SIM_RESTRAIN_B card

Once a similarity group has been defined (with a NOTE BUSTER_SIM_DEFINE card) harmonic restraints coupling the temperature factors can be activated for this group with a NOTE BUSTER_SIM_RESTRAIN_B card:
NOTE BUSTER_SIM_RESTRAIN_B <Group_name> [sigma_B]
where:
<Group_name>: this is a user defined group name that has already defined with a NOTE BUSTER_SIM_DEFINE card or a NOTE BUSTER_SIM_RESTRAIN_JOINT card.
<Sigma_B>: is a positive real number specifying the sigma to be used on the restraint in Å2. Each atom pair in the restraint will contribute separately with this sigma. (Sigma_B): is a optional positive real number specifying the sigma to be used on the restraint in Å. Each atom pair in the restraint will contribute separately with this sigma. If no Sigma_B is specified then a sigma will be obtained from the "WEIGHT NCS" that is current. The TNT "WEIGHT NCS" value is normally set by the autoBUSTER parameter wncs. The default value for wncs is 50). Following the practice of the TNT ncs program Sigma_B is set to (5/0.3)*1/sqrt(wncs) (if not specified on the card). The default Sigma_B is accordingly 2.36Å2.


Joining together different similarity groups with the NOTE BUSTER_SIM_JOINT card (useful for including water in NCS)

The NOTE BUSTER_SIM_JOINT card allows the joining together of two or more similarity groups to form a new group. The card syntax is:
NOTE BUSTER_SIM_JOINT <New_group_name> <Existing_group1> <Existing_group2> ...
where:
<New_group_name>: this is an arbitary user name for the new group. It is usually best to make this informative.
<Existing_group1>: this is a user defined group name that has already defined with a NOTE BUSTER_SIM_DEFINE card
<Existing_group2>: this is a user defined group name that has already defined with a NOTE BUSTER_SIM_DEFINE card
<Existing_group3>: a JOINT card must have at least two groups but can be composed of as many as you want.


Support for old-style methods of defining NCS: CLUSTER and NOTE BUSTER_NCS_SOFT cards

TNT uses a CLUSTER card with CHAINS in it to specify harmonic restraints on positions and temperature factors. gelly will interpret CLUSTER cards by 'translating' them into its own format and should produce identical function values. Details of the translation will be listed in LIST.html. For instance the CLUSTER card:
CLUSTER NTERM RESIDUE 11 - 59 CHAINS A B C D
is translated by gelly:
Translating card 'CLUSTER NTERM RESIDUE 11 - 59 CHAINS A B C D' into gelly format:
NOTE BUSTER_SIM_DEFINE         cluster0001_NTERM { A|11 - A|59 } B C D    # card added - translated CLUSTER
NOTE BUSTER_SIM_RESTRAIN_RMSD  cluster0001_NTERM    # card added - translated CLUSTER
NOTE BUSTER_SIM_RESTRAIN_B     cluster0001_NTERM    # card added - translated CLUSTER 

The previous release of gelly used a NOTE BUSTER_NCS_SOFT card to allow more flexible specification of harmonic NCS restraints. These cards continue to be read and will produce identical results. They are interpreted by 'translating' them into the new format. Details of the translation will be listed in LIST.html. It is advised to switch to the new format as this allows the use of new features such as LSSR.


Specifying target type restraints with gelly cards

Target restraints enable the exploitation of the similarity of the structure under refinement to an already known structure. A command line shortcut sets up a basic default approach. This section explains the gelly cards for target restraints. The cards are both used by the shortcut routine and can be user specified for finer control.

Specifying target structure coordinate files with the NOTE BUSTER_TARGET01 card

The first thing that is necessary for target restraints is load an external target structure to be used. The

NOTE BUSTER_TARGET01 full_path_to_file.pdb
card allows the specification of the coordinates to be used for a target coordinate set.


Defining similarity groups for target restraints with the NOTE BUSTER_SIM_DEFINE card


Page Author: Oliver S. Smart
Please send feedback to: buster-develop@globalphasing.com
Last modification: 23.11.10