Hello all,
Just to tell you that I seem to have solved issue related to multiple spins
vector extraction. I have used the following expressions:
"# Load spins
structure.load_spins(spin_id='@CA', combine_models=False, ave_pos=False)
structure.load_spins(spin_id='@CB1', combine_models=False,
ave_pos=False)
# Set the spin name and then load the NH vectors.
spin.name(spin_id='@CA', name='CA')
structure.vectors(spin_id='@CA', attached='H*', ave=False)
spin.name(spin_id='@CB1', name='CB1')
structure.vectors(spin_id='@CB1', attached='H*', ave=False)
....."
I get information that the spins are all extracted and get S2 values for all
of them.
Cheers
TiagoP
-----Original Message-----
From: edward.dauvergne@xxxxxxxxx [mailto:edward.dauvergne@xxxxxxxxx] On
Behalf Of Edward d'Auvergne
Sent: quarta-feira, 6 de Janeiro de 2010 16:42
To: Tiago Pais
Cc: relax-users@xxxxxxx
Subject: Re: Extracting vectors from multiple spins
Hi,
If you load the PDB file, you need to then need to execute
structure.load_spins() for 'CA' and 'CB' separately. Not all atoms of
the PDB file are treated as spin systems, you must manually specify
these. There should be in the save file spin containers, i.e. XML
elements starting and ending with spin desc="Spin container" name="CA"
num="???"> and </spin> respectively. Only then will you be able to
say that protons are attached to these spins.
Regards,
Edward
2010/1/6 Tiago Pais <tpais@xxxxxxxxxxx>:
Well, the spins of interest are also present in the pdb file previously
loaded.
-----Original Message-----
From: edward.dauvergne@xxxxxxxxx [mailto:edward.dauvergne@xxxxxxxxx] On
Behalf Of Edward d'Auvergne
Sent: quarta-feira, 6 de Janeiro de 2010 16:17
To: Tiago Pais
Cc: relax-users@xxxxxxx
Subject: Re: Extracting vectors from multiple spins
Hi,
This is strange, it should work! Could you file a bug report for
this? If you include data for one or two spins that can reproduce
this, and the script that was used, I should be able to sort out what
is happening very quickly. Though maybe it's just in the script. If
you have the 'CA' and 'CB' spins loaded, the structure.vectors() call
should work. Are these spins loaded into the program before calling
structure.vectors()?
Cheers,
Edward
2010/1/4 Tiago Pais <tpais@xxxxxxxxxxx>:
I have tried that before but it doesn't work - there's the spin.name
issue.
When it is running the second spin there is a warning message:
RelaxWarning: The spin ':140&:W@CD1' is already named. Set the force
flag
to rename
It goes like this for all the residues and then it stops:
The attached atom is not a proton.
RelaxError: No vectors could be extracted.
Cheers
TiagoP
-----Original Message-----
From: Edward d'Auvergne [mailto:edward.dauvergne@xxxxxxxxx]
Sent: segunda-feira, 4 de Janeiro de 2010 10:46
To: Tiago Pais
Cc: relax-users@xxxxxxx
Subject: Re: Extracting vectors from multiple spins
Hi,
You could try something such as:
relax> structure.vectors(spin_id='@CA', attached='H1', ave=False)
and:
relax> structure.vectors(spin_id='@CB', attached='H2', ave=False)
if that is how the atoms are named. Hope this helps.
Regards,
Edward
2009/12/17 Tiago Pais <tpais@xxxxxxxxxxx>:
Hello guys,
Does anyone know if it is possible to extract vectors for multiple spins
in
the same run?
Lets say I would like to extract vectors for example from Ca to H1 and
Cb
to
H2. For the proton attached I imagine one can use the * character but
for
the spin itself I dont see how it can be done.
If anyone has any idea, please reply.
Cheers
Tiago P
**************************************
Tiago Pais, PhD. student
Cell Physiology & NMR
Instituto de Tecnologia Química e Biológica-Oeiras
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RE: Extracting vectors from multiple spins