You are mistaken:  these coordinates appear in the io.mc file you attached in the line

 

“NOsh_setupCalcMGAUTO (nosh.c, 1726):  initial fine mesh lower corner = -40.813 -32.043 -32.3185”

 

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  +1-509-375-3997

http://nabaker.me

 

From: Abhinav kaushik [mailto:abhinav1220k@gmail.com]
Sent: Friday, March 09, 2012 11:36 PM
To: Baker, Nathan
Cc: apbs-users@googlegroups.com; apbs-users@lists.sourceforge.net
Subject: Re: [apbs-users] origin coordinates in a .dx file

 

Hello Nathan,

Thanks a lot for this quick reply. I had calculated electrostatic potential for PDB file 1VINA. As per the output file output.dx the coordinates for origin should be

 "-4.081300e+01 -3.204300e+01 -3.231850e+01" but when I look for similar coordinates in "io.mc" file i found those coordinates neither in "lower corner" section nor in "Grid lower corner" and any other section. io.mc file indicates different coordinates in "lower corner" & "lower grid corner" and my concern is what are those coordinates as they are different from those mentioned in .dx file.

 

Please correct me if I am wrong in understanding the output files. I am attaching the respective files [output.dx (first 100 lines only) and io.mc file]. 

 

Thanking you,

Abhinav Kaushik

Research Fellow,

International center for genetic engg. and biotechnology,

New Delhi, India 

 

On 9 March 2012 20:15, Baker, Nathan <Nathan.Baker@pnnl.gov> wrote:

Hello –

 

Can you please provide the numbers that describe the differences you’re observing?

 

Thanks,

 

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  +1-509-375-3997
http://nabaker.me

 

From: Abhinav kaushik [mailto:abhinav1220k@gmail.com]
Sent: Thursday, March 08, 2012 10:45 PM
To: apbs-users@googlegroups.com
Cc: apbs-users@lists.sourceforge.net
Subject: Re: [apbs-users] origin coordinates in a .dx file

 

 hello Nathan, 

origin must be located on the lower corner but the coordinates mentioned in the origin tag of .dx file does not matches with those mentioned in "io.mc" file. 

thank you ...

 

Abhinav kaushik

Research fellow, 

International center for genetic engg. and biotechnology,

New Delhi, India



On Wednesday, 14 December 2011 21:20:03 UTC+5:30, Baker, Nathan wrote:

Hi Francois --

The origin is the location of the lower corner:  http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/opendx-scalar-data

Thanks,

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997
http://nabaker.me


-----Original Message-----
From: Francois Berenger [mailto:berenger@riken.jp]
Sent: Tuesday, December 13, 2011 11:23 PM
To: apbs-users@lists.sourceforge.net
Subject: [apbs-users] origin coordinates in a .dx file

Hello,

When I read a .dx file generated by APBS, is the origin located at the center of the grid or at one of its corners?

Sorry for the stupid question, I read the doc about the .dx file format but the answer is not obvious to me.

Regards,
Francois.

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On Wednesday, 14 December 2011 21:20:03 UTC+5:30, Baker, Nathan wrote:

Hi Francois --

The origin is the location of the lower corner:  http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/opendx-scalar-data

Thanks,

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997
http://nabaker.me


-----Original Message-----
From: Francois Berenger [mailto:berenger@riken.jp]
Sent: Tuesday, December 13, 2011 11:23 PM
To: apbs-users@lists.sourceforge.net
Subject: [apbs-users] origin coordinates in a .dx file

Hello,

When I read a .dx file generated by APBS, is the origin located at the center of the grid or at one of its corners?

Sorry for the stupid question, I read the doc about the .dx file format but the answer is not obvious to me.

Regards,
Francois.

------------------------------------------------------------------------------
Cloud Computing - Latest Buzzword or a Glimpse of the Future?
This paper surveys cloud computing today: What are the benefits?
Why are businesses embracing it? What are its payoffs and pitfalls?
http://www.accelacomm.com/jaw/sdnl/114/51425149/
_______________________________________________
apbs-users mailing list
apbs-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/apbs-users

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Cloud Computing - Latest Buzzword or a Glimpse of the Future?
This paper surveys cloud computing today: What are the benefits?
Why are businesses embracing it? What are its payoffs and pitfalls?
http://www.accelacomm.com/jaw/sdnl/114/51425149/
_______________________________________________
apbs-users mailing list
apbs-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/apbs-users


On Wednesday, 14 December 2011 21:20:03 UTC+5:30, Baker, Nathan wrote:

Hi Francois --

The origin is the location of the lower corner:  http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/opendx-scalar-data

Thanks,

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  509-375-3997
http://nabaker.me


-----Original Message-----
From: Francois Berenger [mailto:berenger@riken.jp]
Sent: Tuesday, December 13, 2011 11:23 PM
To: apbs-users@lists.sourceforge.net
Subject: [apbs-users] origin coordinates in a .dx file

Hello,

When I read a .dx file generated by APBS, is the origin located at the center of the grid or at one of its corners?

Sorry for the stupid question, I read the doc about the .dx file format but the answer is not obvious to me.

Regards,
Francois.

------------------------------------------------------------------------------
Cloud Computing - Latest Buzzword or a Glimpse of the Future?
This paper surveys cloud computing today: What are the benefits?
Why are businesses embracing it? What are its payoffs and pitfalls?
http://www.accelacomm.com/jaw/sdnl/114/51425149/
_______________________________________________
apbs-users mailing list
apbs-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/apbs-users

------------------------------------------------------------------------------
Cloud Computing - Latest Buzzword or a Glimpse of the Future?
This paper surveys cloud computing today: What are the benefits?
Why are businesses embracing it? What are its payoffs and pitfalls?
http://www.accelacomm.com/jaw/sdnl/114/51425149/
_______________________________________________
apbs-users mailing list
apbs-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/apbs-users