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
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