Subject: Re: [nmr_sparky] convert spectrum of sparky to xeasy
From: Josiah Zayner
Date: Oct 6, 2010

Previous: 761

Try this suite of tools I have used it successfully to convert between many different formats. Look for ucsf2pipe.

http://fermi.pharm.hokudai.ac.jp/olivia/api/index.php/Xyza2pipe_src

Josiah Zayner
University of Chicago



From: Nicholas Fitzkee nfitzkee.lab@...
To: nmr_sparky@yahoogroups.com
Cc: Yibing Wu yibing@...
Sent: Tue, August 31, 2010 7:00:38 PM
Subject: Re: [nmr_sparky] convert spectrum of sparky to xeasy

Hi Yibing,

Funny that this should come up... I just saw a poster at the ICMRBS in Australia last week about precisely this problem. Michael Gryks lab at UConn Health Center has developed a suite of programs called CONNJUR, one of which is a spectrum translator that can interconvert various spectral formats. I dont know if they support UCSF format, but your best bet is probably to ask them. Jay Vyas was the poster presenter, and he seemed really helpful. Here is the CONNJUR web page:

http://connjur.uchc.edu/index.php

On the other hand, you may want to try the NMRPipe mailing list--Frank may be able to point you in the right direction.

Good luck,
Nick

--
Nicholas Fitzkee, Ph.D.
National Institutes of Health
Laboratory of Chemical Physics, NIDDK

e: nfitzkee@...
w: (301) 451-7233
f: (301) 496-0825

On Tue, Jul 13, 2010 at 12:51 PM, Tom Goddard goddard@... wrote:


Dear Sir or Madam,

Id like to ask you a question. I have a very old sparky hsqc ( dated back to 2007 at least) and want to convert it to xeasy format. I tried to load it into Cara and got a error message saying that wrong file format. Do you know if there is other way to do conversion? Is it possible to convert it back to NMRPipe? The raw fid is not possible to find.

I can send you the HSQC if you like.

Thanks a lot in advance,

Yibing

Hi Yibing,

I dont know how to convert from Sparky spectrum format to XEasy format. You can dump the Sparky spectrum data values in binary floating point with no header using the -m option of the ucsfdata command-line program that comes with Sparky (in the sparky/bin directory).

http://www.cgl.ucsf.edu/home/sparky/manual/files.html#ucsfdata

Maybe from that raw format there is a way to produce an XEasy format file.

Tom