Subject: Re: [nmr_sparky] Problem with conversion 3D and 4D spectra from bruker [1 Attachment]
From: Tom Goddard
Date: Oct 28, 2013

Previous: 901

Thanks Mandar. It seems youve shown that Linux Sparky makes and reads spectrum files 2 Gbytes. Thanks for verifying that. If I get time to try a 64-bit Sparky build on Windows or Mac Ill use your file to test it. It is not likely I am going to have time for this since we are not funded to develop Sparky and have many other projects related to our UCSF Chimera visualization program to work on.

Tom



On Oct 25, 2013, at 7:41 PM, Mandar Naik wrote:


Hi Tom,
Although I realized that Sparky wont read zipped file, I wrongly thought the data matrix read after ucsfdata -t will be less demanding for the OS due to the zeroes involved.

I note that I have no issues creating a large 2.8GB ucsf file using bruk2ucsf and reading it in Sparky. I use Sparky 3.113 installed on a 64-bit Mandriva Linux.

I have attached a compressed version of my UCSF file to this email and hope you can use it for testing. The compressed file is hardly 10MB but if that also fails to reach your inbox, you may create such a file on whatever data at your disposal by insane zero-filling. The attached file also has been treated by ucsfdata -t, so please set positive contours to 6E+5 once you unzip and open it in sparky.
With regards
-mandar


On Sat, Oct 26, 2013 at 2:08 AM, Tom Goddard goddard@... wrote:

Hi Mandar,


Thresholding and compressing the spectrum data wont help because Sparky cannot read or write compressed files. The basic trouble is that 32-bit Windows and Mac Sparky versions use offsets into files that only go up to 2 Gbytes. I think the Linux Sparky handles large file offsets but Piotr claims that bruk2ucsf failed on Linux on a large file with the same error message (Failed initializing UCSF file with zeros). So maybe Linux Sparky in fact does not support files larger than 2 Gbytes. I thought Linux Sparky did support it because the Sparky source code has special code for 64-bit file offsets and the Sparky build scripts enable that for Linux. Some testing on Linux would be needed to see if large files work, but I dont have spectra 2 Gbytes to try it.

Tom


On Oct 24, 2013, at 7:51 PM, Mandar Naik wrote:


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