Hi,
This user selected format for the assignment will then be very hard to
automatically handle! If we could find a few example files with
different formats, this might be useful. Or maybe we should tell the
user that a specific format should be used? Do you know if you can
have spaces in this assignment? And is the nlinLS format exactly the
following: http://www.hhmi.umbc.edu/toolkit/processing/nih/nlinLS.html
?
There are 2 things we could do here, use the generic format or a
specific NMRPipe format. The generic format expects different columns
for the molecule name, residue name and number, and spin name and
number - a total of up to 5 columns allowing support for small
molecules, RNA/DNA, and proteins. But it would probably be better to
have a specific reader for this. The reason is because if it is the
above format, then you are only allowed an index as the peak
identifier in this nlinLS file! We would then need an auxiliary file
to identify the INDEX integers. I would recommend an argument
'nlinls_aux_file' to the spectrum.read_intensities() user function.
This would allow this file format to be identified. In this case, the
'mol_name_col', 'res_num_col', 'res_name_col', 'spin_num_col',
'spin_name_col', and 'sep' args will all then refer to the auxiliary
file, and we would also need a 'nlinls_index_col' arg. I.e. the
auxiliary file could look like:
# index res_num spin_name
1 1 C8
2 1 N3
3 2 C6
What do you think? I'm not an expert in this format, so maybe there
already exists some type of auxiliary file.
Regards,
Edward
On Wed, Jul 22, 2009 at 4:56 PM, Douglas
Kojetin<douglas.kojetin@xxxxxxxxx> wrote:
Assignments are found in the ASS column (between TYPE and CLUSTID columns on
the VARS line). As far as I am aware, the actual assignment is typically
user entered and can be whatever is desired. I planned to use a style
similar to Sparky (e.g., M1N-H, M1N-HN, MET1N-H or MET1N-HN).
Doug
On Jul 22, 2009, at 10:34 AM, Edward d'Auvergne wrote:
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>
_______________________________________________________
Reply to this item at:
<http://gna.org/support/?2390>
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Re: [sr #2390] support for nlinLS/NMRPipe peak list