[Chimera-users] Problem: Electrostatic surface coloring
goddard at sonic.net
Fri Sep 24 18:13:37 PDT 2010
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.
> 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)
> 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.
> *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
> _*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.
> mmp92.phi first 5 records:
> reading 60 'qdiffxas: qdiffxs4 with an improved surfacing routine '
> reading 72
> reading 284 ''
> reading 284
> reading 284
> 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.
>> *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.
>>> 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)
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