Hi Damien, Chimera Delphi Controller tries to execute the command-line program "delphi" so it must be in your shell executable search path. On Linux you need it in the directory containing the delphi executable in the PATH environment variable. On the Mac I'm not sure how to set the search path when you start Chimera by double clicking on it. You can still set the shell PATH variable and start Chimera from a terminal like: % path-to-chimera/Chimera.app/Contents/MacOS/chimera The Chimera User's Guide (under Tools / Delphi Controller) says that Delphi Controller does not work on Windows. Maybe it is easier to just edit the line in Delphi Controller code that starts delphi. Just edit line 97 in chimera/share/DelphiViewer/DelphiExecutor.py changing from cmd = "delphi %s > %s" % (self.prmFileName, self.outputFileName) to for example cmd = "/usr/local/bin/delphi %s > %s" % (self.prmFileName, self.outputFileName) giving an explicit path to the Delphi executable. On the Mac this file would be Chimera.app/Contents/Resources/share/DelphiViewer/DelphiExecutor.py Keep the indentation of the Python line the same as this is important. All that said, I would suggest just running Delphi yourself then opening the resulting *.phi file in Chimera. The Delphi Controller Chimera tool was written by a summer intern 5 years ago and has not been worked on much since then. The electrostatic potential file produced by MolMol is not in Delphi format. It uses a MolMol specific format (described at the end of this email) that Chimera does not read. You could hand convert it to another text file format by changing the header, to say the one used by APBS (called OpenDX). But I'd suggest calculating the electrostatic potential with APBS instead. Tom ------- Manual page for MolMol potential file format. NAME ReadPot - read potentials for surface coloring SYNOPSIS ReadPot fileName DESCRIPTION Read a file with potentials, these are used for coloring surfaces. The file must contain values on a grid, the format is: x0 xSize xInc y0 ySize yInc z0 zSize zInc val val val .... where x0, y0, z0 (float) are the coordinates of the grid origin, xSize, ySize and zSize (int) are the sizes of the grid in each dimension, and xInc, yInc and zInc (float) the spacing between two grid points in each dimention. This must be followed by xSize * ySize * zSize values (float), where the x-coordinate is the one that is running the fastest. The potentials will be set for all selected surfaces, but the PaintSurface command has to be given to update the colors. EXAMPLE ReadPot /home/joe/struct/my_pot.dat SEE ALSO CalcPot, AddSurface, SelectPrim, PaintSurface DATE 960509
From: Damien Devos <damien@salilab.org> Date: March 2, 2006 4:04:02 PM PST To: "Eric Pettersen (chimera)" <pett@cgl.ucsf.edu> Subject: delphi in chimera
hi Eric, i'm trying to use delphi in chimera, but couldn't get the delphi controller to help me. alternatively, i used molmol to generate the .phi file and tried to open it in chimera, but i got this message on the reply log:
Done opening /viol1/damien/fgf/molmol/1nuna.pdb Opening /viol1/damien/fgf/molmol/1nuna.phi /viol1/damien/fgf/molmol/1nuna.phi: Record size 539833144 > file size 2725332 Done opening /viol1/damien/fgf/molmol/1nuna.phi
it seems that my .phi file is too big? does this make sense? on the other side, if i could get the delphi controller to work on chimera, that would solve all problems. we have delphi installed localy, but i don't know where to put the path of it and how so that chimera could locate it.
thanks d
-- Damien Devos Andrej Sali Lab California Institute for Quantitative Biomedical Research University of California at San Francisco QB3, Box 2552 1700 4th Street, Room 501 San Francisco, CA 94143-2552 (CA 94158 for courier delivery), USA Phone: +1 (415) 514-4258 Fax: +1 (415) 514-4231 Email: damien@salilab.org URL: http://www.salilab.org