Hi,
I've just looked at the format of the file, and this should be
treatable as the generically formatted peak intensity file. The user
function spectrum.read_intensities() as is can be used for this, as
you can specify the spin information columns (i.e. residue number) and
the data column. I should be able to have this generic file code
functional soon. What would be useful would be to know how
assignments are handled in the nlinLS/NMRPipe format, to handle
everything from small organic molecules, RNA/DNA, to proteins.
Regards,
Edward
On Wed, Jul 22, 2009 at 3:42 PM,
anonymous<NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
URL:
<http://gna.org/support/?2390>
Summary: support for nlinLS/NMRPipe peak list
Project: relax
Submitted by: None
Submitted on: Wednesday 07/22/2009 at 15:41 CEST
Category: None
Priority: 5 - Normal
Severity: 3 - Normal
Status: None
Privacy: Public
Assigned to: None
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Operating System: None
_______________________________________________________
Details:
It would be useful if support for nlinLS/NMRPipe peak lists could
be added to
relax. The nlinLS package is used for lineshape analysis of
peaks. see:
1. http://spin.niddk.nih.gov/NMRPipe/ref/prog/index.html, and
2. the 'relax.tar.Z' example provided on the NMRPipe download page
Input to nlinLS = a series of HSQC data (e.g. T1 or T2 series
data), and a
base spectrum peak list (with optional assignments).
Output = a single peak list with normalized peak intensities from
the data
series.
The nlinLS formatted peak list is different from what relax uses for
NMRView/Sparky/Xeasy. For example, in the sample scripts
relax_fit.py, 10
individual files (peak lists) are read in and associated with
specific
relaxation times. In the case of a nlinLS peak list, a single peak
list with
normalized intensities would be read in, and the relaxation times
would need
to be specified for each normalized intensity column, as compared to
individual files for NMRView/Sparky/Xeasy. A range of column
indexes will
need to be specified to extract the normalized peak intensities.
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Wednesday 07/22/2009 at 15:41 CEST Name: nlin.tab Size:
20kB By:
None
<http://gna.org/support/download.php?file_id=6242>
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Reply to this item at:
<http://gna.org/support/?2390>
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Re: [sr #2390] support for nlinLS/NMRPipe peak list