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.
Hi Nitesh, Could you use the Chimera Help / Report a Bug... menu entry and attach a *.phi file that has this problem? The error message means that Chimera thinks the *.phi file has the wrong format. I'll take a look at it when I get the file. 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.
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_*..... _*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.
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@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_*.....
_*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.
Hi Nitesh, I agree completely with Tom, and would only add that the DelPhi ESP map format (*.phi file) that Chimera reads is from the academic version of DelPhi obtained from the Honig group, as mentioned here: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/filetypes.html#esp> I don't know if this is still true, but at least at some point in the past there was a commercial version of DelPhi that worked with the Insight program, and that may create a different format of ESP map that Chimera does not read. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Sep 24, 2010, at 6:13 PM, Tom Goddard wrote:
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
participants (3)
-
Elaine Meng -
Nitesh Sule -
Tom Goddard