[Chimera-users] Problem: Electrostatic surface coloring

[Tom Goddard]

  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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