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Hi Nitesh,<br>
<br>
I don't use DelPhi so I don't know if your function calls are
right. I am sure that the file you sent has totally different
record sizes than those documented for the *.phi file format. Could
your file actually be a surface file rather than an electrostatic
grid? These questions about whether you are using DelPhi correctly
or why the record structure of your *.phi file does not match the
documented file format are best answered by DelPhi experts rather
than the Chimera developers. Let me know what you find out.<br>
<br>
Tom<br>
<br>
<blockquote type="cite">
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<div style="">Hi Tom,<br>
<br>
The .phi file was generated (as is, no change made in
extension or formatting) by the most current version of
delphi, on windows, (using an input file formatted according
to the sample provided on the website).
<br>
The following lines were used for generating the output:<br>
<br>
out(modpdb, file=xyz.out)<br>
out(phi,file=xyz.grd,format=BIOSYM)<br>
out(phi,file=xyz.phi)<br>
<br>
Do you think there is a problem in these lines? <br>
<br>
I guess if its delphi thats producing incorrectly formatted
output, I should take this problem to them. However, I am able
to use the .phi files generated by delphi to load the phi map
in Grasp2 and color the surface accordingly. So it seems
Grasp2 is able to read this format.<br>
<br>
Regarding the DelphiController bug, I found the same bug
reported a long time ago, and classified as solved.<br>
<br>
Thanks<br>
Nitesh.<br>
</div>
<div style="font-family: Times New Roman; color: rgb(0, 0, 0);
font-size: 16px;">
<hr tabindex="-1">
<div style="direction: ltr;" id="divRpF345304"><font
color="#000000" face="Tahoma" size="2"><b>From:</b> Tom
Goddard [<a class="moz-txt-link-abbreviated" href="mailto:goddard@sonic.net">goddard@sonic.net</a>]<br>
</font><br>
</div>
<div>Hi Nitesh,<br>
<br>
The file you sent me mmp92.phi is not in the correct
format for a Delphi *.phi file. This file is supposed to
contain the 3-d grid of electrostatic potential values.
Here's what the Delphi documentation says the format should
look like<br>
<br>
<a class="moz-txt-link-freetext"
href="http://www.csb.yale.edu/userguides/datamanip/delphi/manual.html#_*4_*._*2_*._*7_*"
target="_blank">
http://www.csb.yale.edu/userguides/datamanip/delphi/manual.html#_*4_*._*2_*._*7_*</a>.<br>
<br>
_*4_*._*2_*._*7_*. FILE.phi:
<p>Unformatted file</p>
<pre> character*20 toplabel
character*10 head,character*60 title
real*4 phi(65,65,65)
character*16 botlabel
real*4 scale, oldmid(3)
</pre>
This means the record sizes in the file should be 20, 70,
65*65*65*4, 16, 4*4. The last record is the "params"
mentioned in the error message you get from Chimera and
should be size 16 (or in newer Delphi versions 20 or 36).<br>
<br>
The record sizes for your mmp92.phi file are 60, 72, 284,
284, 284, ... totally different. I was not able to fine
what kind of Delphi file has those record sizes. The total
file size 1472120 bytes is also about half a normal
potential file. Records shown below. Did you rename this
file to have the *.phi suffix?<br>
<br>
Someone will respond to your Delphi Controller bug report
when it is assigned. It used to be that this tool did not
work on Windows. Possibly that was fixed since I no longer
see that limitation mentioned in the Chimera User's Guide.<br>
<br>
Tom<br>
<br>
<br>
mmp92.phi first 5 records:<br>
<br>
uplbl<br>
reading 60 'qdiffxas: qdiffxs4 with an improved surfacing
routine '<br>
morelabels<br>
reading 72
'\x00\x00\x00\x00\x04\x00\x00\x00\x00\x00\x00\x00hQPBhQPBhQPB\x00\x00\xb4B\x00\x00\xb4B\x00\x00\xb4B\xe65\t\xbf\xf9\xe0N?\xbc-\xb0\xbe\x00\x00\x80?\x93\xe9\xdb\xbe\x15"j?F\x00\x00\x00F\x00\x00\x00F\x00\x00\x00'<br>
skip<br>
reading 284 ''<br>
botlbl<br>
reading 284
"\xffE\x819\xf2\x8c\x8e9o\xe0\x9c9\x18I\xac9\xbf\xcd\xbc9pr\xce9\x069\xe19\xc3\x1f\xf59\xb0\x10\x05:I\x1a\x10:\x98\xa5\x1b:$\xa9':\x91\x184:\xfe\xe4@:\x18\xfcM:\xc8H[:\x14\xb3h:^\x1fv:\xf0\xb7\x81:\xebA\x88:\x0b\x9c\x8e:\xfc\xb3\x94:\x7fv\x9a:1\xd0\x9f:n\xad\xa4:\xf5\xfa\xa8:g\xa6\xac:s\x9e\xaf:/\xd3\xb1:\x067\xb3:\x8f\xbe\xb3:\x02a\xb3:\xf8\x18\xb2:\xeb\xe3\xaf:\xe4\xc2\xac:\x9d\xba\xa8:\xf5\xd2\xa3:+\x17\x9e:\x0b\x96\x97:\xd6`\x90:\xb0\x8b\x88:\xa5,\x80:\xa4\xb6n:\x8da\\:\xe8\x8cI:|l6:72#:5\x0f\x10:Ec\xfa9|\x89\xd59\x99\xde\xb19\xdc\xa7\x8f9xB^9^\xf8
9m\x81\xcf8\x8c[K8\\\xb3\x186\x17\x19&\xb8U\xc0\xa1\xb8ul\xe7\xb8\xe9
\x12\xb9\xa3E,\xb9\xc3SB\xb9\x94\x82T\xb9\xa5\x0fc\xb9\xb5=n\xb9\x01Rv\xb9\x12\x94{\xb9^K~\xb9\xc7\xbe~\xb9\xf32}\xb9"<br>
params<br>
reading 284
'V\xa8\x8a9\x90\x19\x999?\xb5\xa89\x8e\x85\xb99\xd1\x92\xcb9\xd0\xe2\xde9Ox\xf39S\xa9\x04:\x846\x10:\x00_\x1c:\x81\x1b):\x0fb6:h%D:QUR:\xfb\xdd`:\x02\xa8o:\xb3\x98~:\xe9\xc8\x86:\xdb8\x8e:\xf3\x89\x95:c\xa8\x9c:h\x7f\xa3:n\xf9\xa9:8\x00\xb0:\x96}\xb5:\x8c[\xba:\x04\x85\xbe:\x01\xe6\xc1:ll\xc4:\x94\x08\xc6:!\xad\xc6:\x00P\xc6:\xc1\xea\xc4:Gz\xc2:\xc5\xff\xbe:I\x80\xba:\xb3\x04\xb5:\x18\x9a\xae:\x15Q\xa7:c=\x9f:\xc6u\x96:\xba\x13\x8d:\x1a2\x83:\xf4\xdaq:\xcd\xc5\\:\xf6^G:G\xe01:\xce\x80\x1c:\x12u\x07:\xac\xda\xe59\x9d+\xbe9\xad)\x989\x0e0h9\x92Z$9BR\xca8Ss+8}"&\xb7)\xf8i\xb8\xc5\xeb\xca\xb8\xaeY\x0b\xb9,I,\xb9\x87pH\xb9y\x08`\xb9\x0bQs\xb9`I\x81\xb9.\r\x87\xb9\x87\x1b\x8b\xb9"\x9d\x8d\xb9\xb8\xba\x8e\xb9\t\x9c\x8e\xb9Fh\x8d\xb9'<br>
Error reading file mmp92.phi, format delphi<br>
Parameter record size 284 must be 16 or 20 or 36<br>
<br>
<br>
<blockquote type="cite">
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rgb(0, 0, 0); font-size: 13px;">
<div style="">Hi Tom,<br>
<br>
Thanks for getting back. I have attached the .phi file
(mmp92.phi) as well as the reply log file (phi bug).<br>
<br>
Incidentally, I am also unable to run Delphi through
Chimera using the DelphiController (though the Delphi
executable runs fine by itself). I recently submitted
a report regarding this with the reply log attached,
but the attachment probably didn't make it through. I
am also attaching this log file, named "bug".<br>
<br>
Thanks again.<br>
Regards,<br>
Nitesh.<br>
</div>
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0, 0); font-size: 16px;">
<hr tabindex="-1">
<div id="divRpF584702" style="direction: ltr;"><font
color="#000000" face="Tahoma" size="2"><b>From:</b>
Tom Goddard
<br>
<b>Sent:</b> Tuesday, September 21, 2010 1:54 PM<br>
<b>To:</b> Nitesh Sule<br>
<b>Subject:</b> Re: [Chimera-users] Problem:
Electrostatic surface coloring<br>
</font><br>
</div>
<div>Hi Nitesh,<br>
<br>
Turns out our report-a-bug system is not handling
file attachments properly due to some problem with
our bug tracking server. So email the *.phi file
directly to me.<br>
<br>
Tom<br>
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<div style=""> Hi,</div>
<div style=""><br>
</div>
<div style="">I am having trouble getting
chimera to open .phi files, with the following
reply: </div>
<div style="">"Error reading file xyz.phi,
format delphi</div>
<div style="">Parameter record size 284 must be
16 or 20 or 36"</div>
<div style=""><br>
</div>
<div style="">The .phi file was generated using
delphi, and works fine when opened with
Grasp2. </div>
<div style="">Can someone please help me with
this? </div>
<div style=""><br>
</div>
<div style="">On a slightly related note, I am
also unable to use the delphi controller in
Chimera, with the message:</div>
<div style="">"Delphi exited with
status -1073741794". I am not sure if this is
a bug. I can provide more details from the
log.</div>
<div style=""><br>
</div>
<div style="">Chimera version: 1.4.1 (build
29977)</div>
<div style=""><br>
</div>
<div style="">Thanks</div>
<div style="">Nitesh.</div>
</div>
<br>
</blockquote>
<br>
</div>
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