<div dir="ltr">Tom,<div><br></div><div>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.</div><div><br></div><div>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.</div><div><br></div><div>Emil Alexov</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, Jan 7, 2020 at 6:38 PM Tom Goddard <<a href="mailto:goddard@sonic.net">goddard@sonic.net</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div style="overflow-wrap: break-word;">Hi Shailesh,<div><br></div><div>  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.</div><div><br></div><div>  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.</div><div><br></div><div><span style="white-space:pre-wrap">       </span>Tom</div><div><br><div><br><blockquote type="cite"><div>On Jan 7, 2020, at 10:55 AM, Shailesh Kumar Panday  wrote:</div><br><div><div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;background-color:rgb(255,255,255)">Hello Chimera Developers,</div><div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;background-color:rgb(255,255,255)"><br></div><div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;background-color:rgb(255,255,255)">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.</div><div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;background-color:rgb(255,255,255)"><br></div><div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;background-color:rgb(255,255,255)">Thank you,</div><div style="font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt;background-color:rgb(255,255,255)"><span><br></span></div><div style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><div id="gmail-m_-4577221536631503951Signature"><div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt"><span><div style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:12pt"></div></span><span><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.33px"><span style="font-family:Arial,Helvetica,sans-serif">Shailesh Kumar Panday</span><br></div></span><span></span><span></span><span><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.33px"><span style="font-family:Arial,Helvetica,sans-serif">Postdoctoral Fellow</span></div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.33px"><span style="font-family:Arial,Helvetica,sans-serif">Computational Biophysics and Bioinformatics Lab</span></div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.33px"><span style="font-family:Arial,Helvetica,sans-serif">Department of Physics and As</span></div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.33px"><span style="font-family:Arial,Helvetica,sans-serif">Clemson University, SC 29634</span></div><div style="color:rgb(34,34,34);font-family:Arial,Helvetica,sans-serif;font-size:13.33px"><span style="font-family:Arial,Helvetica,sans-serif">Lab:<span> </span></span><a href="http://compbio.clemson.edu/" style="color:rgb(17,85,204)" target="_blank"><span style="font-family:Arial,Helvetica,sans-serif">http://compbio.clemson.edu</span></a></div><br></span></div></div></div><span id="gmail-m_-4577221536631503951cid:3DE2CFCA-3DBD-4BD1-985A-9AEEBB123E77@cgl.ucsf.edu"><DelphiViewer.tar></span><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">_______________________________________________</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none;float:none;display:inline">Chimera-dev mailing list</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><a href="mailto:Chimera-dev@cgl.ucsf.edu" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">Chimera-dev@cgl.ucsf.edu</a><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;text-decoration:none"><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant-caps:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev</a></div></blockquote></div><br></div></div></blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div>Emil Alexov</div><div>Professor, Department of Physics</div><div>Professor, Department of Material Sciences</div><div>Professor, School of Nursing: Healthcare Genetics</div><div>Faculty Scholar at Clemson School of Health Research</div><div>Clemson University</div><div>Lab: <a href="http://compbio.clemson.edu" style="font-size:12.8px" target="_blank">http://compbio.clemson.edu</a></div></div></div></div></div></div>