[chimera-dev] Update to DelphiViewer Chimera plugin

[Emil Alexov]

Tom,

This seems to me is misunderstanding. We purposely decided to make the new
delphi version to write PHI map file into CUBE format, because this is the
format that all existing visualization packages take. This is documented in
DelPhi manual and nowadays our users indeed prefer CUBE format versus the
old style binary file.

However, if this is too much trouble for Chimera maintenance and
development, we will make an effort to include binary option in the new
delphi. Let's us know what are your thoughts about this.

Emil Alexov

On Tue, Jan 7, 2020 at 6:38 PM Tom Goddard <goddard at sonic.net> wrote:

> Hi Shailesh,
>
>   Thanks.  I see your changes to the Chimera DelphiViewer plugin make it
> write out a Gaussian cube file instead instead of a .phi file.  While that
> helps a little it would be much better if new DelPhi wrote out a .phi file
> following the online documentation for that file format.  This should be
> trivial to do even from C++ (while the original format used Fortran
> records, they are just a 4 byte count for each record, followed by the
> binary data).  Having DelPhi write out a different incompatible .phi file
> as it dose not breaks all software that used that format.  We can't take
> the tens of thousands of copies of Chimera out of circulation that read
> .phi files.  Also even with your change to make Chimera run DelPhi
> outputting a cube file, users will run DelPhi outside of Chimera, then try
> to open the .phi file and get an error.
>
>   If the .phi format is just going to remain broken with new DelPhi
> versions writing an incompatible format I think we just need to remove it
> from Chimera and our new program ChimeraX.  If your new .phi format is in
> use by new software and cannot be fixed I'd suggest that you use a
> different file suffix so software can correctly read the new or old format.
>
> Tom
>
>
> On Jan 7, 2020, at 10:55 AM, Shailesh Kumar Panday  wrote:
>
> Hello Chimera Developers,
>
> We have made some changes in the DelphiViewer plugin to enable reading and
> writing Delphi potential in "Gaussian cube grid" format. The older binary
> "Delphi or GRASP potential" format files are no longer supported in Delphi.
> Hence plugin was unable to parse the potential file, the attached version
> fixes this issue.
>
> Thank you,
>
> Shailesh Kumar Panday
> Postdoctoral Fellow
> Computational Biophysics and Bioinformatics Lab
> Department of Physics and As
> Clemson University, SC 29634
> Lab: http://compbio.clemson.edu
>
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>
>

-- 
Emil Alexov
Professor, Department of Physics
Professor, Department of Material Sciences
Professor, School of Nursing: Healthcare Genetics
Faculty Scholar at Clemson School of Health Research
Clemson University
Lab: http://compbio.clemson.edu
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