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The Tools Menu

The tools menu regroups tools that are less frequently used than those present in the display window (or just once for each layer). This avoid screen cluttering, and allows a better explanation of their function than an icon would.

  • Compute H-bonds
    H-bonds can be estimated even if no H atoms are present in the file. Please note that H-bonds are evaluated for the current molecule only . To change the current molecule, see the control panel section.
    H-bonds are computed only between different groups, which means that intramolecular H-bonds are not detected.

    H-bonds are detected on the basis of distance, atom type (as defined in ref.[1]) and angle.
    When a same group is at H-bond distance of several other atoms, all possible H-bonds are drawn, and no attempt to choose the best one is done.
    H-bonds are detected if an H is in a 1.2 up to 2.76 A range of a "compatible" donor atom. If the PDB file does not include H atoms coordinates, H-bond are detected when the distance between donor and acceptor is from 2.35 up to 3.2 A. H-bonds that are within this distance range are drawn as green dotted lines, weaker H-bonds (extra allowed distance: 0.05 angstroms by default) appear in grey.
    The distances settings can be modified using the previous menu item (H-bonds detection threshold).

    Note: HETATM atom types are not defined and are at best assigned as "plain" N, O, H and so on... It means that no difference is made between a "N" group (that can H-bond) and a "NT" group (that cannot H-bond): all "N" atoms are noted "N_" and designed internally as H-bond capable. A direct consequence is that some impossible H-bonds can be drawn from or to HETATM
  • Compute Molecular Surface
    The probe size is 1.4 Angstroms and all atoms have a fixed radius. It is currently not possible to change this. The only value that can be altered is the smoothness (quality) See the Surface Preferences Menu. Quality 1 and 2 use one grid point every 1.4 Angstrom, as does Quality 0. Quality 3 and 4 use a grid twice as dense. Quality 5 and 6 use a grid three times finer than quality 1 and 2.
    Note that a finer triangulation (resulting in more triangles) is done for Qualities 2 4 and 6 than for Quality 1,3 and 5.
    Note that Hydrogens atoms are currently ignored during the surface computations. Depending on the Preferences Settings, selected residues might also be ignored form the computation, which is useful to have a closer look at active sites, or protein-protein interaction surfaces.
  • Compute Electrostatic Potential
    Use the Electrostatic Potential Preference Menu to define how it should be computed. Once it is computed, if it has been kept, it will be possible to alter the potential contouring value using the keyboard up and down arrows. Parameters can also be adjusted using the 'Electron Density and Potential Maps' window accessible from the Wind Menu.
  • Triangulate Maps
    This tool can be used to convert an electron density map (or potential) into a triangulated surface. The current contouring level will be used. The advantage is that it will be much faster to display, but the tradeoff is that it will no longer be possible to alter the contouring values in real time.
  • Compute Threading Energy
    Update the mean force potential energy, whose individual results are displayed in the Align Window as a curve (click on the little arrow located at the top of the Align Window to view the curve). See the User Guide for more information on this tool.
  • Compute Energy (Force Field).
    The Energy is computed with a partial implementation of the GROMOS96 force-Field. You can choose what kind of interaction you want to compute (bond, angles, improper, electrostatic... however, Unless you are just interested to identify bad geometry, all parameters should be checked for proper meaningful computation). In addition, make sure that the "Show Report" option is checked to obtain a full text report with detailed energy for each residue. Residues with obvious problems will be highlighted in red, and clicking on any line will center the view on the faulty residue and display only immediate neighbors.
    Note that a '*' in front of a line means that there are bad non-bonded interactions (that is two residues are bumping into each other) whereas a '>' in front of a line means distorted geometry.
    Note that it is also possible to color the protein by energy using a gradient from blue (good) to green and green to red (bad) to quickly highlight regions of the protein with issues. The Energy report is saved in Swiss-PdbViewer 'temp' directory, so if you want to keep it for later, make a copy of it before Quitting Swiss-PdbViewer (Quitting erases temp. files)
  • Energy Minimization.
    Energy Minimization is performed with the partial implementation of the GROMOS96 force-Field. (see Compute Energy above). In this implementation, all computations are done in vacuo, without reaction field. It is recommended to enable the non-bonded interaction computation, unless you just want to quickly regularize the geometry of a residue.
    Note that it is currently not possible to minimize compounds within Swiss-PdbViewer.
  • Energy Minimization (for one compound).
    This is performed by submitting the selected compound (only one at a time) to the PRODRG server maintained at the University of Dundee by Alexander Schuettelkopf and Prof. van Aalten who kindly allowed direct submission from Swiss-PdbViewer to their service. Typically, compounds can be loaded as .SDF files, or imported from PubChem using the File:Import Menu
  • Fix selected sidechains
    Quick and Dirty: This will browse the rotamer library and replace the sidechain of any selected amino-acid by the best rotamer accordingly to the same simple scoring scheme used as when residues are mutated (see mutation user guide for details). Exhaustive Search: This will assess all rotamer combinations with the Gromos96 force field. Do not select too many residues at the same time, as this can result in a combinatorial explosion. To cancel the operation, hold down the 'esc' key until the process stops. Simulated Annealing. This will assess a sample of all rotamer combinations, using a simulated annealing function which combines the simple scoring scheme with the Gromos96 forcefield. Contrarily to the exhaustive search, it is not guarantee to reach the minimum energy configuration but will be much faster when several residues are selected.
  • Apply Transformation
    This will let you enter a transformation matrix. This can be useful when you want to precisely translate or rotate a molecule.
    Note that only selected groups are transformed. Usually such matrices are present in PDB files (for example 4mdh) and describe a specific transformation. In the 4mdh case, it is the transformation needed to superpose the chain B onto the chain A.
    Note: You don't have to retype the matrix values, all you need to do is click on the ORIGX, MTRX line of a pdb file (or the SMTRY or BIOMT lines of REMARK 290 or 350) to "feed" the values into this dialog.
    Note: To display the pdb file as text, click on the small text icon of the toolbar.
    Note: there is no check that the matrix you enter is valid.
    Note: You can undo a transformation by enabling the "reverse transfomration" checkbox (however this will not let you undo a projection! So be careful.
  • >Build Crystallographic Symmetry
    This will open the "crystsim.txt" file present in the "_stuff_" directory. If Swiss-PdbViewer cannot guess your space group, you might have to locate it yourself. Then click on the header of your space group (that is displayed in red) if you want to build all symmetries, or just on the crystallographic operator you want to use. A new layer with the transformed protein will be created. This tool is useful for crystallographers, to inspect crystalline contacts. This is best used in conjunction with the "select Groups Close to an other layer" item of the select menu.
    Note: invoking this tool with the Control Key down will let you enter a symmetry operator from a text window.
    Note: you might want to check the 'Draw Unit Cell' option of the Electron Densit Maps Preferences. If this is not drawn, Click on the CRYST line of the PDB file to force the use of those parameters.
  • Translate Along Unit Cell Axis.
    The previous menu will not necessarily create a symmetric protein contained within the unit cell. Use this menu to translate it into your unit cell.
    Note: invoking this tool with the Control Key down will translate a copy of the layer, leaving the current layer untouched instead of moving the current one.
  • Detect Secondary Structure
    This tool will force the reevaluation of the secondary structure for the current layer. This can be useful after a modification of a Phi/Psi angle (for example from altering points from the Ramachandran Plot)
  • Generate 3D Motifs From Selection
    This menu writes a 3D motif search definition based on the residues selected and the various distances that have been measured using the distance measuring tool. The file can be modified by the user and used to search 3D motifs in proteins. Refer to the tutorial for further details.
  • Search 3D Motifs In Current Layer
    This menu will ask the user for a file containing a 3D motif search definition and report each match for the current layer. Clicking on a hit will select the corresponding residues and highlight the distance constraints. Refer to the tutorial for an exmaple.
  • Submit 3D Motif Search Against Subset of PDB
    This menu will do the same as the previous one, except that it will search a non-redundant set of PDB files for hits that match the 3D motif definition. The search is performed at the Swiss Institute for Bioinformatics Vital-IT supercomputing center. Results are submitted to a queue, so a unique ID is returned to the user for further reference (using the File:Import dialog). However, as soon as some hits are identified, they are displayed in the user interface for further visualization. As sometimes, partial results are reported, it is possible to use the 'Submitted Job' submenu from the Swiss-Model Menu to request the latest version of the results. Refer to the tutorial for further details.
  • Randomize Atoms Positions Of Selected Groups
    This will randomly translate all atoms of the selected groups by the desired amount (Angstroms) This can be used before an energy minimisation, or simply for teaching purposes, but be warned that it cannot be undone.
  • Set as Alpha Helix
    This will set the Phi/Psi angles of the selected aminoacids to 60 deg. and 40 deg. respectively
  • Set as Beta Sheet
    This will set the Phi/Psi angles of the selected aminoacids to 120 deg and 120 deg respectively
  • Set Phi/Psi
    This will let you set arbitrary Phi/Psi angles for the selected aminoacids.
    Note that you can also modify Phi/Psi angles directly by dragging points around on the Ramachandran plot.
  • Move C-term part during Phi/Psi Changes
    When checked, this option will move all downstream amino-acids from the one whose Phi or Psi angle is modified, leaving the N-term part of the protein untouched.