Bodil

Last updated: 19 February 2009.

Frequently asked questions

I read a structure into Bodil, but I cannot see anything in the 3Dview window. Is the structure really read in?

Answer: If you see the name of the structure in the StructureEditor, then the structure has been read in. To make the structure visible in the graphics window, center it: 3Dview [MENU] Mouse - Center and double click in the black 3Dview window.

I selected a residue in the 3Dview window. I then tried to hide it using StructureEditor [MENU] Display - Hide, but I could not hide the residue. Why?

Answer: This is a question that can come up when there are more than one structure or sequence read into Bodil. The StructureEditor window is divided into two parts: the left and the right panel. It is only possible to give commands to a structure, which is currently highlighted on the left panel and whose hierarchical tree is shown on the right panel of StructureEditor. This applies not only to the hide function, but also to all the other functions in StructureEditor.

Why does HOMODGE not work?

Answer: First check that you have read into Bodil the template structure (coordinates). Then check that the sequence of the template structure is located first in the sequence alignment and that the sequence of the model is second.

Why does MALIGN not work? Why MALIGN aligns only a part of the alignment?

Answer: If you have cut the sequences or for some other reason selected a range, MALIGN will perform alignment for the selected range. To cancel the range, choose from AlignmentEditor [MENU] Range - Full and MALIGN will align the whole alignment.

Is it possible to do all rotation and translation of a molecule in the 3Dview just with the keyboard?

Answer: The rotation amount can be adjusted. Add a configuration file entry:

	  [GV2]
	  TurnDown         = 90.0
	  TurnUp           = 90.0
	  TurnLeft         = 90.0
	  TurnRight        = 90.0

where the numbers are degrees. Configuration file is a text file, like: ~/.Bodil/*.conf
The next version will use:~/.Bodil/Preferences.conf to override other *.conf files in that directory.

Is there a way for the user to add additional (non-standard) amino acids to the Bodil internal residue database so that the non-standard amino acids would be recognized as residues and not ligands?

Answer: For the moment the residue list is fixed. The only option is to edit PDB file in order to create "Standard" residues. Simply rename those residues. Extra atoms will get in ok, but bond types may be wrong.

Is it possible to use the functions of Bodil from the command line? For instance to superimpose a set of 100 protein chains.

Answer: No, it is not yet possible. You can, however, superimpose "Vertaa" several chains in one go. Select one protein as "fixed" and everything else as "superimpose these". Each chain will be superimposed pairwise on the "fixed".

Is there a way to display inter- or intramolecular hydrogen bonds?

Answer: Yes, but the bonds have to be defined first, either in the PDB file (CONECT records) or manually in the 3Dview. Choose 3Dview[MENU] Add - Bond. That will create a bond for each measured "Distance" shown in the window. Bond type has to be changed manually, one by one, in the StructureEditor. The bond types are about the same as used by the Tripos SYBYL Mol2 file format, i.e.
case '1': return "Single";
case '2': return "Double";
case '3': return "Triple";
case 'N': return "Amide";
case 'A': return "Aromatic";
case 'H': return "Hydrogen";
case 'S': return "Disulphide";
case 'I': return "Saltbridge";

Most bonds are drawn similarly to single bonds. To change the color of the bond, toggle from PartColor to SingleColor in the StructureEditor. Click with the RMB on the bond object to see the popup menu for each object. The default, "PartColor", is to use atom colors (half and half).

How to search for a specific amino acid with the Query tool?

Answer: The identification of a residue in a PDB file (ignoring the chain ID) contains the residue name, the residue sequence number, and the insertion character. Thus, the residue number is in practice a value that has an integer part and a character part. The character part is usually a space ' '. In Bodil, empty chain IDs ' ' are converted to/from underscore '_', but insertion characters are not.
If you searching for e.g. the residue ALA1, you should type the following string to the Query form: 'ALA1.'
The '.' indicates any or no characters.

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