Subject: Re: [nmr_sparky] How to handle pseudo 3D data in planes from Pipe?
From: Woonghee Lee
Date: May 15, 2019

Previous: 1459 Next: 1461


Hi James,

There are two ways:

1. Fix headers of ft2 files by using sethdr from NMRPipe.
2. Treat as a regular 3D until you get a .ucsf file and split by planes using -ps option of ucsfdata or easy_ucsfdata.

Best,
Woonghee


On Wed, May 15, 2019 at 10:29 AM Gibson, James gibsoj3@... [nmr_sparky] nmr_sparky@yahoogroups.com wrote:
 

Borrowed somebody elses pulse sequence in Bruker, which was only written in 2D data but is psuedo 3D data.  Used a conversion script in nmrPipe to get it into planes (where each plane is an HSQC-like spectrum), and has the data name plane006.ft2 etc.  But when I tried to convert it with pipe2ucsf, I got an error about the expected file size, where it appears the ucsf file is expecting the whole 3D series.  I tried to see if I could get around it using the easy pipe2ucsf utility from the NMRFAM window, but got an error that the ucsf file was not created.  I assume that is the same error.  Is there a way around this?

I was able to turn the planes into a full 3D and convert that into a ucsf file for Sparky to read.  But then, I didnt understand how to get at each of my planes.  I can rotate it around so I have the HN projection, but then the 3rd dimension, which is pseudo appears to be lost.  If this is possible instead of the above, perhaps this would be the better solution?

Thanks for your help,

James