[Chimera-users] Problem: Electrostatic surface coloring

Fri Sep 24 18:13:37 PDT 2010

  Hi Nitesh,

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.

      Tom

> 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 at 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.
>>>
>>
>

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