[Chimera-users] delphi potenital map viewing

Thomas Goddard goddard at cgl.ucsf.edu
Fri Dec 5 13:30:28 PST 2003

Hi Klaas,

  The Delphi Viewer is the only tool that can color a molecular surface
according to the potential value.

  Can you email me the Python traceback you get when the "_cubes error: ..."
occurs?  This shows exactly where in the code the error happened.  You find
it by looking at Favorites/Reply Log.

  Having the traceback alone might be enough for me to figure out and
correct the problem.  If you could put the phi file on the web so I could
download it I would almost certainly be able to figure out the problem.

  The Delphi Viewer is supposed to be able handle maps of any size.
It will be much slower than volume viewer, but it should not generate
an error with a large map.


> Date: Fri, 05 Dec 2003 21:10:20 +0100
> From: Klaas Decanniere <Klaas.Decanniere at pandora.be>
> Reply-To: Klaas.Decanniere at pandora.be
> To: Thomas Goddard <goddard at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] delphi potenital map viewing
> Thomas Goddard wrote:
> >Hi Klaas,
> >
> >  The size of the Delphi potential map Chimera can display is only
> >limited by the size of your computer memory.
> >
> >  If you open a large map it does not get shown immediately if the map
> >is larger than 1 Mvoxels (~100^3). 
> >  
> >
> When I tried using the "delphi viewer" option, I get _cubes error: grid 
> index out of range
> Using the volume viewer I can indeed load everything.
> Is there a way to tie the volume viewer thing to a molecular surface? 
> With a colour gradient showing different levels of potential? (As in the 
> Molecular surface option in the Delphiviewer)
> Or maybe I can save the subsampled map somehow and then read it into the 
> delphiviewer thing?
> Thanks again for your help.
> Klaas
> P.S.: I like the program more each day.
> P.P.S.: If you ever have a day with nothing to do: the automatic 
> fetching of pdb files doesn't work for me as I'm behind a proxy server.

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