VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 08 2004 - 17:49:37 CDT

Miguel,
  Can you email me a copy of the map file that fails to load with the
VMD 1.8.2 version of the grdplugin? Also, if you can send a native
GRID file, and a URL for their file format specification documents,
we can see how difficult it would be to write a native plugin for that
file format. The new coloring feature works for _all_ supported volumed
data file formats, and is completely independent of where the data came from.
The main limitation in the current implementation of the coloring feature
is that my rendering code only does orthogonal cells presently, I'm still
working on finishing the OpenGL code to do the texturing for non-orthogonal
cells.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Apr 08, 2004 at 11:43:03PM +0100, Miguel Ortiz Lombardía wrote:
> Hi John,
>
> I would like to try this capability indeed. However, I'm not sure
> this may solve my problem. This is because the "delphi" map I'm
> trying to read was not produced by delphi, but by another program,
> called GRID, that has an option for writing its maps in such
> format.
>
> In VMD 1.8.2 I can read delphi maps produced by delphi, but when
> I try one of this GRID maps in "delphi" format I get the error:
>
> Error: uplbl does not match.
> Unable to open file with plugin of type grd
>
> However, I know these very same maps can be opened with other programs
> interfacing with delphi maps. It seems to me that it has to do with
> checks the grd plugin may make on the header of the map, rather than
> with its actual format.
>
> The ideal situation would be to be able of reading the "native"
> GRID maps, because when this program produces a "delphi" map it has
> some drawbacks, the biggest being a limitation in size of the box
> to 64x64x64 Angstroem. Not suitable for medium-big proteins. In its
> own format, this problem doesn't exist. Could this routine to colour
> representations by volumetric data be adapted to such maps (provided
> we found the definition of that format, of course)? Or is it "hard-
> wired" for delphi and the like?
>
> Thank you very much for your interest and for your help.
>
> Sincerely,
>
> Miguel
>
>
> John Stone <johns_at_ks.uiuc.edu>, 08/04/2004:
> > Date: Thu, 8 Apr 2004 16:48:43 -0500
> > From: John Stone <johns_at_ks.uiuc.edu>
> > To: Miguel Ortiz Lombardía <mol_at_ysbl.york.ac.uk>
> > Cc: vmd-l_at_ks.uiuc.edu
> > Subject: Re: vmd-l: mapping delphi potential maps on surfaces
> > Mail-Followup-To: John Stone <johns_at_ks.uiuc.edu>,
> > Miguel Ortiz Lombardía <mol_at_ysbl.york.ac.uk>,
> > vmd-l_at_ks.uiuc.edu
> > User-Agent: Mutt/1.3.19i
> >
> >
> > Miguel,
> > The existing released versions of VMD don't have any built-in features
> > for coloring representations by volumetric data, but if you would like to
> > try one a pre-release version of VMD 1.8.3 that has this capability,
> > let me know and I'll supply you with a test version that has this coloring
> > capability. If you want to use the existing versions of VMD, then the
> > 'potsurf' script. The potsurf script works by assigning potential values
> > to each atom using the "beta" field, it then colors it by "beta".
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Thu, Apr 08, 2004 at 10:03:00AM +0100, Miguel Ortiz Lombardía wrote:
> > > Hi everyone,
> > >
> > > I have a pdb and a delphi potential map ("grasp" format, read with
> > > the grdplugin)
> > >
> > > I can load both, and see the information in the potential map using,
> > > for example, the VolumeSlice or IsoSurface representations.
> > >
> > > My question is: how I do map this potential on the surface (MSMS or
> > > whatever) of the molecule?
> > >
> > > The script potsurf seems to use the pdb file that delphi output,
> > > instead of the potential map itself (but not sure about this)
> > >
> > > Thanking you in advance!
> > > Best regards,
> > >
> > > Miguel
> > > --
> > > Miguel Ortiz Lombardía
> > > email: mol_at_ysbl.york.ac.uk
> > > http://www.ysbl.york.ac.uk/~mol
> > > -----------------------------------------------------------------------
> > > Our business in life is not to succeed, but
> > > to continue to fail in good spirits. R.L. Stevenson
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> ~~~~~~~~~
>
> --
> Miguel Ortiz Lombardía
> email: mol_at_ysbl.york.ac.uk
> http://www.ysbl.york.ac.uk/~mol
> -----------------------------------------------------------------------
> Our business in life is not to succeed, but
> to continue to fail in good spirits. R.L. Stevenson 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078