DelPhi Notes

Look at the official DelPhi web site for more documents.

Release Notes

Example Files

How To Use DELPHI in the IU MolViz Facility

• A pdb (Protein DataBank) file contains the atomic coordinates of your molecule. This file can be generated from InsightII, acquired from the Protein DataBank, etc.

• A prm file lists the aprameters required for the DelPhi calculation. Download the PTI prm file as an example. Make sure that the name of your prm file has the same prefix as your pdb file (e.g., pti.pdb and pti.prm are OK).

  To generate a InsightII-compatible grid file, which lists the net charge at each grid point around your molecule, specify:

  out(phimap,format="BIOSYM",file="molecule_name.phi")

  in your prm file.

• A siz file lists the size of atomic radii. Download the PTI siz file as an example. Make sure that the name of your siz file has the same prefix as your pdb file (e.g., pti.pdb and pti.siz are OK). Note that you can change or add to this file as needed.

• A crg file lists charges for each atom type. Download the PTI crg file as an example. Make sure that the name of your crg file has the same prefix as your pdb file (e.g., pti.pdb and pti.crg are OK). Note that you can change or add to this file as needed.

DelPhi is executed via a command line as in

delphi prm > logfile &

prm is your prm file as described above. logfile is a file to log any messages from the program.

While this command also works on stereo3, delphi64 is a faster program on this workstation. delphi64 is a compiled version for 64-bit operting systems. DelPhi is executed onstereo3 as in

delphi64 prm > logfile &

The following stats are taken from the PTI example run on O2 and Octane SGI workstations.

How To Make Grid Files For InsightII

In the file.prm file, specify:

out(phi,format="BIOSYM",file="molecule_name.phi")

This will generate a InsightII-compatible grid file (listing charges at each point in the grid about your molecule) when you run DelPhi.

After DelPhi is finished,

1. Start InsightII.
2. Read in your molecule.
3. Click on the Grid icon on the left side of the InsightII window.
4. click on Get in the Grid menu.
5. Type in File Name (i.e., molecule_name.phi)
6. Turn on the Reference flag (click on the blue box next to "Reference" to make it turn yellow).
7. Type in your Reference (your molecule)

1. click on Molecule/surface and generate a surface. The Solid connolly surface at High resolution looks best, but it can be slow to create & rotate this surface. Choose a lower-resolution and/or choose a Quick surface for faster display (but always choose to make a Solid surface).

2. To color the surface with the DelPhi charges, click on Molecule/Color, and color the Surface by the Grid color method The CHARGE_SPECTRUM is a good template for the Spectrum_name. Choose your grid for the Scalar_Grid_Name.

3. To edit the spectrum (e.g., the maximum and minimum charge values), click on Spectrum/Edit.