From: Cesar Avila (cavila_at_fbqf.unt.edu.ar)
Date: Sat Apr 21 2007 - 20:05:42 CDT

Dear John,
The problem seems to be related with the specific version of Delphi I am
using. Apparently VMD has no problem reading the maps generated by the
official Delphi latest version from Honig's lab. Nevertheless I had some
trouble using that delphi version with my system (may be size related). I
reported this bug to Delphi's crew and after a while they kindly sent me
new binaries able to deal with my system. Now that I compare the files
generated by both versions I realized that the new maps are twice as large
as the original phi maps. I don't know where the differences are between
both binaries ( I don't have the source code ). I will try to get in touch
once again with Delphi's code mantainer to ask about this changes.
Best Regards
Cesar

>
> 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
>