31 March 98
by N.Guex
Building
Tools
Swiss-PdbViewer provides various tools to manipulate a protein.
- Build loop
Given two amino-acids as anchor points, several loops will be constructed de novo, and you can then pick your favorite one very easily. See the tutorial to know how to proceed.
- Scan loop Database
Given two amino-acids as anchor points, a database of folds will be scanned to find compatible fragments. The matching loops are then presented to you for further selection. See the tutorial to know how to proceed.
- Find Best Fitting Peptides
Given a poly-Ala fragment, an electron density map, and the primary sequence of the protein you want to solve, an attempt to find the best fitting fragments will be done. See the tutorial to know how to proceed.
- Break Backbone
You will be asked to pick either a N atom or a C atom of the backbone, and this latter will be broken at this point. This can be very useful to prevent the whole molecule to move when a Phi/Psi angle is modified.
- Ligate Backbone
This will try to ligate the backbone of any unlinked amino-acid to anoter amino-acid.
- Add Residue
Amino-acids can be added either at the N-terminal or at the C-terminal of a peptide fragment, depending on which backbone atom you pick (N or C).
- Add Bond
This will let you pick two atoms to be bonded. This can be useful when no CONECT ionformation are present in a pdb file, as the automatic connection feature is not guaranteed to be able to figure out all the connections.
- Add H-bond
Useful for final polish of a scene, when the Compute H-bond tool has missed the very special H-bond you wanted to render! Note that this is not saved in a file, and will be lost each time you recompute the H-bonds.
- Add H-bond
Useful for final polish of a scene, when the Compute H-bond tool has missed the very special H-bond you wanted to render! Note that this is not saved in a file, and will be lost each time you recompute the H-bonds.
- Add all H
not available in this version.
- Add polar H
not available in this version.
- Add H2O
A Water molecule (H2O) will be added at 2.6Å of the picked atom, in a location where it does not clashes too much and is able to do H-bonds. This is useful for crystallographers that want to add water. You can then select this new water molecule, and move it around to place it into the density. There is no automatic placement into the density yet, but it will come later.
- Remove Bond
Opposite of Add Bond!
- Remove H-Bond
Opposite of Add H-Bond!
- Remove H
Remove all H (but the one present on HETATM; because some might be wrongly assigned as H by the automatic atom type detection whereas they are in fact something else.) If you really want to remove all H, use the control key while invoking this tool.
- Remove nonPolar H
Same as before, but only for non-polar H. This allows to do c leaner pictures of NMR structures (for example).