Hi Nick,
I'll answer your questions below:
1) Default lists created by Sparky look like this:
Assignment w1 w2 Data Height
R1N-H 126.139 8.573 108076
Q4N-H 118.070 8.861 50515
F5N-H 119.682 7.577 111977
T6N-H 113.163 8.827 95306
R7N-H 120.731 8.903 108430
A8N-H 126.058 10.299 92981
Q9N-H 118.747 8.300 127858
W10N-H 122.375 9.005 102254
F11N-H 121.361 8.698 114173
A12N-H 122.049 8.175 59426
I13N-H 118.046 7.753 129168
Q14N-H 111.972 7.184 73155
H15N-H 106.081 7.773 119082
I16N-H 122.326 8.294 156604
S17N-H 120.624 7.734 133194
L18N-H 128.309 8.660 163834
N19N-H 115.816 8.450 241597
It depends on how you assigned the peaks. If you use the full
3-letter code, then it'll look like your example below. When I use
Sparky, in the 'at' window I use text such as 'TRP100' for the group.
You can pretty much use what you like, but it's difficult for relax to
then match everything up. It would be good to have proper residue
identification and then conversion of the different residue name
formats, but this is quite complex if you take modified residues, DNA,
RNA, sugars, and organic molecules into account - something which
cannot be ignored.
According to the relax manual, we need to convert lists to the following
format:
Assignment w1 w2 Data Height
ARG1N-HN 126.139 8.573 108076
GLN4N-HN 118.07 8.861 50515
PHE5N-HN 119.682 7.577 111977
THR6N-HN 113.163 8.827 95306
ARG7N-HN 120.731 8.903 108430
ALA8N-HN 126.058 10.299 92981
GLN9N-HN 118.747 8.3 127858
TRP10N-HN 122.375 9.005 102254
PHE11N-HN 121.361 8.698 114173
ALA12N-HN 122.049 8.175 59426
ILE13N-HN 118.046 7.753 129168
GLN14N-HN 111.972 7.184 73155
HIS15N-HN 106.081 7.773 119082
ILE16N-HN 122.326 8.294 156604
SER17N-HN 120.624 7.734 133194
LEU18N-HN 128.309 8.66 163834
ASN19N-HN 115.816 8.45 241597
To match the PDB file later on, this is important. At some point a
conversion will need to be performed. No one has had a need yet, but
anyone could contribute such conversion code. It would require a set
of conversion tables added to 'generic_fns/mol_res_spin.py', and some
new user function arguments for all of the data loading functions to
active the conversion only when asked. This is a perfect small
project for any power users out there ;)
First, do we need to add any unused/unassigned residues like this or is this
irrelevant:
PRO2N-HN None None None
PRO3N-HN None None None
?
Those shouldn't appear in the 2D peak lists and are not needed. There
are no proline backbone N spin systems with proton attached (I would
hope), so data for such spin systems need not be loaded. relax will
handle all of such issues automatically.
2) Does anyone have a script to automatically convert Sparky lists to the
right format for relax? This is a tedious process to run manually.
I don't have one, but maybe someone else on this list does? Such a
script, if written in Python, could be absorbed into
'generic_fns/mol_res_spin.py' and then be part of the core of relax
(as I described above).
3) After modifying the sample script to run a simple R1 analysis with our
own modified Sparky lists and PDB, the 'python relax_fit.py' command yielded
the following error:
File "relax_fit.py", line 26, in <module>
pipe.create('rx', 'relax_fit')
NameError: name 'pipe' is not defined
Any idea what's going on? Are we using the command correctly?
From the 'Scripting' section of the introductory chapter of the relax
manual, it says:
What ever is done within the prompt is also accessible through
scripting (Figure 1.2). Just type your commands into a text file ending
in ‘*.py’ and then at the terminal type
$ relax your script.py
The user functions in the script are specific to relax and will not be
available from the Python interpreter.
I hope this helps.
Regards,
Edward
Re: R1, R2 and/or NOE Analysis with Relax