Hi Dungeng,
Welcome to the relax mailing lists! For your questions, firstly can
you type 'relax' from anywhere and relax executes? Which operating
system is this running on, and which version of relax? I'll answer
your questions below:
On 27 April 2010 19:33, D. Peng <dgpeng@xxxxxxxxx> wrote:
Hi, Guys
I tried to use this software to calculate the hetNOE based on my with and
without NOE TROSY spectra. I had assigned all the peaks I need in both
reference and with-NOE spectra, exported the two lists as ref.list and
sat.list.
Followed is what I did this morning in the folder where "relax" is in.
1, copy ref.list, at.list and pdb file to the relax folder
These should be in their own folder. They shouldn't be in the relax
folder - this is reserved for the files belonging to the program.
2, follow the protocol of calculating NOE in the chapter 4 in the relax.pdf
file
2.1, pipe.create(‘NOE’, ‘noe’)
Are you using the relax prompt or relax scripts?
2.2,structure.read_pdb(file=‘*’)
#if I typed in '*.pdb' instead of '*', then error came
This is not correct. You need to specify the PDB file directly, i.e.
type out its full name.
2.3, structure.load_spins(spin_id=‘@N’)
# what I am concened is how to avoid 2.2 and 2.3, since it will be no use in
calculating NOE values
This is just one way of loading the sequence information into relax.
You need not use a PDB file. You can use a file with columns of
sequence information instead. See the help for the sequence.read()
user function. All the information you need is there.
2.4, noe.read(file=‘ref.list’, spectrum_type=‘ref’)
noe.read(file=‘sat.list’, spectrum_type=‘sat’)
#both of them did not work.
#error information:
Traceback(most recent call last):
File "<console>", line 1, in <module>
AttributeError:Noe instance has no attribute 'read'
# I checked the "alphabetical listing of user functions", there is no
detail of this function.
The problem here is that the manual must be a little behind. This has
recently changed, and the user function you now need is called
"spectrum.read_intensities()". More up to date is the
sample_scripts/noe.py file. You can copy that file and modify it to
your needs. That one should work, and the manual should be updated to
reflect this :S If you could, it would be useful for others if a bug
report was made describing the problem with the manual. This will
also remind me to fix these things. Bug reports can be submitted at
http://gna.org/bugs/?func=additem&group=relax, and all relax bugs can
be viewed at http://gna.org/bugs/?group=relax (change the 'Display
Criteria' to see everything).
Sorry to raise so many problems. If you guys know how to solve them, please
write back to me.
It's not a problem at all. If you have any other questions, don't
hesitate to ask.
Regards,
Edward
Re: Some questions about using relax