Subject: Re: [nmr_sparky] Problem with conversion 3D and 4D spectra from bruker
From: Mandar Naik
Date: Oct 24, 2013

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I am wondering if removing spectral noise by ucsfdata -t will help this issue or not. The file size remains identical after this treatment but the output file can be compressed a lot more by gzip.
With regards
-mandar


On Fri, Oct 25, 2013 at 2:29 AM, Tom Goddard goddard@... wrote:
 

There are no 64-bit Sparky distributions on the Sparky web site.  Im pretty certain about that.  I compiled those, although it was more than 5 years ago, so memory cant be trusted.


I am pretty certain that Windows 32-bit Sparky cannot access parts of any spectrum file beyond 2 Gbytes from the start of the file, and cannot write files larger than 2 Gbytes.  I think Linux can access and write files larger than 2 Gbytes.  On Mac Im not certain because I dont know if the flag to enable 64-bit file offsets was used during the Mac compilation.  My guess is that Intel Mac Sparky does use 64-bit file offsets, but PPC Mac Sparky does not.

  Tom



On Oct 24, 2013, at 10:24 AM, wrote:

 

 I suppose something like that. But I know that people  use a sparky to work with very large file (tens of GB ore more), and they use a bin pack directly from sparky web site, and i am pretty sure that it is 32 bit version (i dont see 64 compiled version). But they   use probably another program to make ucsf. So i suppose problem is only with conversion script (bruk2ucsf). Do You think the same will be with pipe2ucsf? 


Best wishes

Piotr



---In nmr_sparky@yahoogroups.com , nmr_sparky@yahoogroups.com wrote:

The Sparky distributions are all 32-bit progr! ams (from 2008 when 64-bit was not common).  In 32-bit file offsets go up to only 4 Gbytes.  In fact they are signed integers which limits them to accessing 2 Gbyte files.  On Linux there is some special code in Sparky to support 64-bit file offsets.  So I believe that in Linux Sparky you can convert and use files larger than 2 Gbytes.  But I am quite sure Windows and Mac have a 2 Gbyte limit.

I believe the Sparky code could be recompiled 64-bit on Mac, Windows and Linux and that would make files larger than 2 Gbytes work.  But it is not simple to compile Sparky.  The source code is available on the Sparky web site, but the build scripts are a mess, so youd have to be pretty resourceful to get the compilation to work.

Tom


On Oct 24, 2013, at 4:26 A! M,  wrote:

 

Dear colleagues

I have a strange problem with conversion 3D and 4D  data from bruker format to ucsf using bruk2ucsf script. Everything work well for spectra smaller then ca. 2GB. But for larger file i cant convert file, i have massage : Failed initializing UCSF files with zeros. This is a big problem for hight resolution 3D and 4D spectra obtained by NUS. Sometimes it is possible to open properly  3rrr or 4rrrr file just in sparky, but in most case half of the spactra is missing. I am sure that spectra are processed correctly becouse i can check it   in TopSpin.   I use sparky 3.113 on windows (I also try convert file on linux but i have exactly the same problem) ant TopSpin3.2.

How i can fix this problem??