[chimera-dev] Update to DelphiViewer Chimera plugin

[Tom Goddard]

Hi Emil,

  We will update Chimera to use CUBE format with DelPhi before our next release.

  The link I sent you to the Chimera bug report gives the full DelPhi output and DelPhi version that produced the incorrect file.

	http://plato.cgl.ucsf.edu/trac/chimera/ticket/17169 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/17169>

I've attached it here as a text file.  I asked the user to contact your lab a several days ago but I don't know if they have time.

Thanks!

	Tom



> On Jan 8, 2020, at 9:56 AM, Emil Alexov <ealexov at g.clemson.edu> wrote:
> 
> Hi Tom,
> 
> Please switch to CUBE format. Regarding the user, who knows how the file was generated. Let them contact us and we will figure out what was wrong. In any case, I agree with you that wrong format file should not be generated. Ask the user to contact us and we will let you know the outcome.
> 
> Emil
> 
> On Wed, Jan 8, 2020 at 12:33 PM Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
> Hi Emil,
> 
>   I agree it is probably a misunderstanding.  The CUBE format is fine and I can switch new Chimera versions to use it.  The trouble is that a user sent me a *.phi file written by DelPhi 7 that does not follow the format specification for .phi.
> 
>  <http://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/ticket/17169/default.phi>http://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/ticket/17169/default.phi <http://plato.cgl.ucsf.edu/trac/chimera/raw-attachment/ticket/17169/default.phi>
> 
> as part of Chimera bug report
> 
> http://plato.cgl.ucsf.edu/trac/chimera/ticket/17169 <http://plato.cgl.ucsf.edu/trac/chimera/ticket/17169>
> 
> This is a binary file so it is not an ascii CUBE file.  Looking at the strings at the beginning of the file it appears to be .phi format without required record lengths.  If this change to the DelPhi .phi file output was not intended then either it should be fixed to output a correct .phi format, or DelPhi should be made to not output .phi at all (just give an error that it is no longer supported).  As it is now, DelPhi outputs an incorrect file.
> 
> 	Tom
> 
> 
>> On Jan 8, 2020, at 3:48 AM, Emil Alexov wrote:
>> 
>> 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 <mailto: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 <http://compbio.clemson.edu/>
>>> <DelphiViewer.tar>_______________________________________________
>>> Chimera-dev mailing list
>>> Chimera-dev at cgl.ucsf.edu <mailto:Chimera-dev at cgl.ucsf.edu>
>>> http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev <http://www.rbvi.ucsf.edu/mailman/listinfo/chimera-dev>
>> 
>> 
>> -- 
>> 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 <http://compbio.clemson.edu/>
> 
> 
> -- 
> 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 <http://compbio.clemson.edu/>
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