P I S A
Protein Interfaces, Surfaces and Assemblies
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P I S A |
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Protein Interfaces, Surfaces and Assemblies
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Input Data Page displays the summary of input data and provides controls for re-running PISA calculations with modified parameters, which may be needed in rare circumstances.
| File | Full path to file in local file system, or "PDB=>1xyz" if coordinate file was downloaded from the PDB. |
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| Title | Structure title as read from the input file |
| Space group | Space symmetry group |
| Resolution | Structure resolution, in angstroms |
| Cell | Unit cell parameters: α, β, γ, a, b, c |
| Cell volume | Volume of unit cell in cubic angstroms |
| Protein chains | Total number of protein chains in asymmetric unit |
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| DNA/RNA chains | Total number of nucleic acid chains in asymmetric unit |
| Ligands | Total number of ligands in asymmetric unit |
| NCS-mates | Total number of monomeric units in ASU, related by non-crystallographic symmetry |
The above means that ligands SO4 and GOL are excluded from PISA assembly analysis, and ligands are processed in automatic mode.
In most instances, no modification of default actions are required. QtPISA automatically excludes cofactors (small molecules, ligands) that are commonly used to aid crystallisation. Such substances provide additional (unnatural) binding between monomeric units in crystal, and for this they may cause wrong conclusions on oligomeric states of macromolecules.
The ligand processing mode is a technical parameter, which is reserved for expert use. Due to highly non-linear complexity of PISA algorithms, it may slow down considerably if the number of ligands is high. There is no ultimate threshold for the acceptable number of ligands, as it depends also on crystal structure and composition. In order to cope with this complexity, PISA may choose to fix all or some of ligands to macromolecules they contact, observing that any single ligand can be fixed only to one macromolecule. The makes the macromolecules with fixed ligands effectively a combined monomeric unit, which decreases computational complexity. In most cases, the only side-effect of this procedure is in changed free energies of complex dissociation within overall accuracy of PISA calculations. In very rare instances, the side effect may need to be verified. For this, at user's request, PISA can process ligands in 3 modes:
| Auto | PISA decides automatically, which ligands should be fixed to macromolecules, and which ones should be considered as free entities. This is the default mode, and it is good in most cases. |
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| Fix all | All ligands are mandatory fixed to macromolecules. |
| Free all | No ligands are fixed to macromolecules. |
At this point, the user can choose which ligands to exclude from the analysis as not belonging to the biological system, by ticking in the corresponding checkboxes. Next, the user may choose whether to fix ligands to macromolecules or not, or let PISA to decide on this, by making the appropriate selection in the Ligand processing combobox. After making changes, click button Rerun to (re-)start calculations. If necessary, both changes and restart may be done while PISA calculations are still running. Note that QtPISA does not have any means to terminate on-going calculations, but, instead, it allows for working with partial results, and it is Ok to quit QtPISA before the calculations finish.
In which cases default options for ligand treatment should be
adjusted?