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CCP4i: Graphical User Interface |
| Structure Analysis Module |
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The layout of each task window, i.e. the number of folders present, and whether these folders are open or closed by default, depends on the choices made in the Protocol folder of the task (see Introduction). Although certain folders are closed by default, there are specific reasons why you should or may want to look at them. These reasons are described in the Task Window Layout sections below.
The Areaimol task has a number of protocols to calculate the solvent accessible surface areas (ASA) and area differences for a variety of situations.
Accessible Surface Area: calculates the accessible surface area for all atoms of the requested type (protein or solvent). The effects of intermolecular contacts due to symmetry-related molecules can also be included.
Treatment of waters: normally ASA is calculated for protein atoms only and waters (solvent) are ignored in the calculation. ASA can also be calculated specifically for waters: if waters are treated as 'solvent' then the ASA of individual waters will only be affected by the presence of neighbouring protein atoms; if they are treated as 'protein' then individual ASAs will also be affected by neighbouring waters.
Area Differences For Protein: differences in ASA correspond to buried area due to the interaction in question:
Oligomer formation: the supplied coordinate file should contain coordinates which compromise a single protein 'unit' (i.e. monomer). Define the symmetry operations to use to generate the oligomers. The first area calculation will be for the oligomer, the second will be for the monomer. The differences will be the change in ASA on the monomer when it is oligomerised.
Crystallographic contacts: the supplied coordinate file should contain coordinates which compromise a single copy of the protein. Define the spacegroup which specifies the crystallographic symmetry. The first area calculation will be for the protein in the crystal, the second will be for the protein only. The differences will be the change in ASA on the protein when it is placed within the crystal.
Ligand/subunit binding: the supplied coordinate file should contain the bound protein-ligand complex. Define the chains in the file which constitute the ligand only. The first area calculation will be for the protein-ligand complex, the second will be for the protein only. The differences will be the change in ASA on the protein when the ligand is bound.
Molecular binding: the supplied coordinate file should contain the chains making up two or more molecules. Define molecules in terms of the chains in the file which constitute each molecule of interest. Calculations will then be performed for each pair of molecules to determine the area buried in the interaction.
Area Differences For Waters: useful for looking for buried waters:
See program documentation: AREAIMOL.
Task for computing various types of contacts in protein structures. The task runs with a choice of NCONT or CONTACT/ACT as the underlying program. These programs give very similar analyses, but each one may be more convenient in particular circumstances. Both NCONT and CONTACT use a bricking algorithm in which atoms are segregated into 6x6x6 Å boxes and contact searching is limited to neighbouring boxes; this is very fast.
NCONT performs different kinds of searches with respect to what symmetry operations and lattice translations are applied, and this should be selected in the Protocol folder. See the NCONT documentation for a detailed explanation.
CONTACT reads a standard Protein Data Bank file which must contain SCALE cards if looking for metal-ligand or intermolecular contacts.
For CONTACT, the maximum residue number is 9000. Maximum number of atoms is 48000. There is no limit for NCONT.
Features to look out for in the Contact Task are:
| Folder title | NCONT | CONTACT/ACT | Importance | Comment |
|---|---|---|---|---|
| Symmetry operations | Y | Y | Use spacegroup or list of operators to define symmetry operations | Spacegroup required if looking for all contacts. Choice of spacegroup or list of operators required if looking for metal-ligand or intermolecular contacts. |
| Atom Selection | Y | Y | Define atoms involved in contacts | In NCONT mode, the program uses the atom selection syntax described in the PDBCUR documentation. This can be added directly, or a template created with the boxes provided and then edited if necessary. |
| Metal contact parameters | N | Y | Define metal coordination geometry | Define type of metal and expected metal-ligand distance |
See program documentation: NCONT. CONTACT. ACT.
PISA (Protein Interfaces Surfaces and Assemblies) is a program for analysing protein structures to look for assemblies of subunits, and the resulting subunit interfaces and surfaces. This interface enables the standalone version of the Pisa program to be run on a local machine.
The interface is run interactively in an iterative manner:
PISA (Protein Interfaces Surfaces and Assemblies) is a webservice hosted at the EBI which allows various analyses of protein structures. Structures can be taken from the PDB archive by specifying an accession code, or can be uploaded from the user's computer.
This is an alternative to the Pisa task run on the local machine. See also the EBI PISA webservice page: PISA
Generate graphs of average B-factor versus residue for each chain in the PDB file. This task will launch loggraph directly to give a quick view of the graphs. The graphs can still be viewed later via the View Files from Job button applied to the task results.
See program documentation: BAVERAGE.
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