Hi Tom,

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). 
The following lines were used for generating the output:

out(modpdb, file=xyz.out)
out(phi,file=xyz.grd,format=BIOSYM)
out(phi,file=xyz.phi)

Do you think there is a problem in these lines?

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.

Regarding the DelphiController bug, I found the same bug reported a long time ago, and classified as solved.

Thanks
Nitesh.

---

From: Tom Goddard [goddard@sonic.net]

Hi Nitesh,

  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

    http://www.csb.yale.edu/userguides/datamanip/delphi/manual.html#_*4_*._*2_*._*7_*.

_*4_*._*2_*._*7_*. FILE.phi:

Unformatted file

 character*20 toplabel
 character*10 head,character*60 title
 real*4 phi(65,65,65)
 character*16 botlabel
 real*4 scale, oldmid(3)

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).

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?

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.

    Tom


mmp92.phi first 5 records:

uplbl
reading  60 'qdiffxas: qdiffxs4 with an improved surfacing routine       '
morelabels
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'
skip
reading  284 ''
botlbl
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"
params
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'
Error reading file mmp92.phi, format delphi
Parameter record size 284 must be 16 or 20 or 36

Hi Tom,

Thanks for getting back. I have attached the .phi file (mmp92.phi) as well as the reply log file (phi bug).

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".

Thanks again.
Regards,
Nitesh.

---

From: Tom Goddard
Sent: Tuesday, September 21, 2010 1:54 PM
To: Nitesh Sule
Subject: Re: [Chimera-users] Problem: Electrostatic surface coloring

Hi Nitesh,

  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.

    Tom

 Hi,

I am having trouble getting chimera to open .phi files, with the following reply: 

"Error reading file xyz.phi, format delphi

Parameter record size 284 must be 16 or 20 or 36"

The .phi file was generated using delphi, and works fine when opened with Grasp2. 

Can someone please help me with this? 

On a slightly related note, I am also unable to use the delphi controller in Chimera, with the message:

"Delphi exited with status -1073741794". I am not sure if this is a bug. I can provide more details from the log.

Chimera version: 1.4.1 (build 29977)

Thanks

Nitesh.