VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Apr 23 2007 - 14:55:59 CDT

Cesar,
  Is the double precision map format now a standard feature of Delphi,
or is this a custom or "hack" of Delphi that won't be used by others?
We could probably expand the delphi related VMD plugins to handle
more variations of the format, but this is only worth doing if they
intend to begin storing double precision maps in a standard version
of Delphi. If you can ask about some of these details and get back
to us that would be very helpful in deciding how to best handle it.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Apr 23, 2007 at 03:12:49PM -0300, Cesar Luis Avila wrote:
> Dear John,
> Walter Rocchia, from Honig's lab, told me that the version he sent me
> was compiled to store the maps using double precision.
>
> >Dear Cesar,
> >
> >to the best of my remembering, in order to maintain the backword
> >compatibility, no change has been made on the routine that generates
> >the phi map. The only thing that comes up to my mind is that the
> >version I've sent you was compiled with the Double precision data
> >structure option. This might explain the double dimension of the file.
> >
> >You might try this and let me know whether it works, possible
> >solutions are using the single precision delphi, or modifying the code
> >so that, regardless the precison of the data structure,
> >the phi map is saved in single precision format.
> >
> >Let me know
> >Yours
> >Walter
>
> John Stone escribió:
> >Cesar,
> > If you're using the binary ("unformatted") Delphi format, you'll
> >need to use grdplugin to load them. Since you got an error trying
> >the grd plugin, it seems that there's a limitation or weakness in the
> >implementation of the grdplugin reader. If you can send me the delphi
> >map I'll have a look at this. What version of Delphi made the map file?
> >Someone else recently ran into trouble loading a binary delphi map, I'm
> >still waiting for details on their Delphi version etc as well.
> >Anyway, if the map file is small enough to gzip and email to me,
> >please send it to me that way, otherwise you could post it in the
> >VMD Public project BioFS area in the "testfiles" directory:
> > http://www.ks.uiuc.edu/Research/vmd/alpha/
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Fri, Apr 20, 2007 at 08:36:48PM -0300, Cesar Luis Avila wrote:
> >
> >>Dear all,
> >>I was wondering if PHI maps calculated with delphi could be seen using
> >>VMD. I had no problem in the past with maps calculated with APBS, but
> >>with delphi I have tried both standard and GRASP formated phi maps
> >>(generated with delphi) and none could be loaded with any of delphi file
> >>types. Here are some of the errors reported by the different plugins.
> >>-------
> >>ERROR) Unable to open file with plugin of type delphibig
> >>Unexpected end-of-file.
> >>Couldn't read fort.14
> >>-------
> >>graspplugin) First characters of file don't look like a GRASP file
> >>ERROR) Reading raw graphics failed.
> >>-----------
> >>Unable to open file with plugin of type grd
> >>Error: non-cube grid
> >>----------
> >>
> >>The box is composed of 155 grid points per side.
> >>The output file from delphi seems to be in binary format.
> >>Any suggestion on how to generate the phi map for later use with vmd?
> >>I am using lastest stable version of vmd 1.8.6
> >>Regards
> >>Cesar
> >>
> >
> > 

-- 
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