Hi Ed,
all residues, except for the glycines (G2, G7, G8, G14, G26) should have
their values such as CSA etc. set.
I've attached the python script to this email, together with the .save
file that gets read in by it, and the .results file. The .save and
.results are from a previous relax run in which I have fitted
microdynamic parameters to the relaxation data. Now I want to see how
well the relaxation data belonging to the fitted microdynamic parameters
fit to the measured original data...
On a related note: The error occurs in both relax 1.2.2 and relax 1.2.3.
I tried testing relax 1.2.4., but It won't start up on my machine giving
me the following error:
[h.schirra@djc-montecristi ~/kalata]$ ~/relax-1.2.4/relax
Traceback (most recent call last):
File "/home/h.schirra/relax-1.2.4/relax", line 70, in ?
from io import IO
File "/home/h.schirra/relax-1.2.4/io.py", line 36, in ?
from os import F_OK, access, devnull, makedirs, remove, stat
ImportError: cannot import name devnull
Is that a relax issue, or shall I kick our IT guys for a dodgy python
installation??
Cheers, and thanks in advance!!
Horst Joachim
----------------------------------------------------------------
/ Dr. sc. nat. Horst Joachim Schirra Phone: (+61)7/3346-2021 /
/ Queensland Smart State Fellow Fax: (+61)7/3346-2101 /
/ Institute for Molecular Bioscience /
/ University of Queensland email: h.schirra@xxxxxxxxx /
/ Brisbane QLD 4072, Australia http://www.uq.edu.au/~uqhschir /
----------------------------------------------------------------
----- Original Message -----
From: Edward d'Auvergne <edward@xxxxxxxxxxxxx>
Date: Friday, July 7, 2006 6:22 pm
Subject: Re: [bug #6288] errors in value.copy and value.delete, possibly
sequence gap related...
> Hi,
>
> Horst, I just have a few quick questions about the bug report.
> Residue 3 appears to be selected yet not have a CSA value. Is this
> correct? The fix should be relatively easy, it's probably that the
> CSA value of 'None' needs to be caught and handled properly. Another
> thing is, would you be able to attach your relax script to the bug
> report. It will help to work out why the global_flag variable has not
> been set yet (it should exist).
>
> Thanks,
>
> Edward
>
>
> On 7/4/06, anonymous <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
> >
> > URL:
> > <http://gna.org/bugs/?func=detailitem&item_id=6288>
> >
> > Summary: errors in value.copy and value.delete,
> possibly> sequence gap related...
> > Project: relax
> > Submitted by: None
> > Submitted on: Tuesday 07/04/2006 at 06:34 CEST
> > Category: None
> > Priority: 5 - Normal
> > Severity: 4 - Important
> > Status: None
> > Privacy: Public
> > Assigned to: None
> > Originator Name: Horst Joachim Schirra
> > Originator Email: h.schirra@xxxxxxxxx
> > Open/Closed: Open
> > Release: 1.2.2
> > Operating System: GNU/Linux
> >
> > _______________________________________________________
> >
> > Details:
> >
> > Hi Ed,
> >
> > Using relax 1.2.2. under linux.
> >
> > I'm currently trying to backcalculate some raw relaxation data
> (R1 etc) from
> > a set of microdynamic parameters that I got.
> >
> > 1) When I do
> >
> > value.copy(run_name, 'test', 'csa')
> > to copy the parameters from the run where they originated into
> the new run
> > 'test', I get the following error:
> >
> > Traceback (most recent call last):
> > File "<console>", line 1, in ?
> > File "/home/h.schirra/relax_1.2.2/prompt/value.py", line 99, in
> copy> self.__relax__.generic.value.copy(run1=run1, run2=run2,
> param=param)> File
> "/home/h.schirra/relax_1.2.2/generic_fns/value.py", line 82, in copy
> > set(run=run2, value=value, error=error, param=param, index=i)
> > File "/home/h.schirra/relax_1.2.2/specific_fns/base_class.py",
> line 154, in
> > set
> > setattr(self.relax.data.res[self.run][index], object_name,
> float(value) *
> > scaling)
> > TypeError: float() argument must be a string or a number
> >
> > same happens with most other parameters (e.g. s2, s2f, etc).
> >
> > When I check with
> > value.display('test', 'csa')
> >
> > what has arrived, I get:
> >
> > Num Name Value Error
> > 1 CYS 2.4999999999999998e-05 None
> > 2 GLY None None
> > 3 GLU None None
> > ....
> >
> > HINT: Gly 2 is not selected in the relax run. I assume the error
> lies> somewhere in that copy vcan't deal yet with gap residues...
> >
> > Sequence:
> >
> > relax> sequence.display(run_name)
> > Number Name Selected
> > 1 CYS 1
> > 2 GLY 0
> > 3 GLU 1
> > 4 THR 1
> > 5 CYS 1
> > 6 VAL 1
> > 7 GLY 0
> > 8 GLY 0
> > 9 THR 1
> > 10 CYS 1
> > 11 ASN 1
> > 12 THR 1
> > 13 PRO 1
> > 14 GLY 0
> > 15 CYS 1
> > 16 THR 1
> > 17 CYS 1
> > 18 SER 1
> > 19 TRP 1
> > 20 PRO 1
> > 21 VAL 1
> > 22 CYS 1
> > 23 THR 1
> > 24 ARG 1
> > 25 ASN 1
> > 26 GLY 0
> > 27 LEU 1
> > 28 PRO 1
> > 29 VAL 1
> > ===================================================
> >
> >
> >
> > 2) Related. when I try to delete the original relaxation data
> from run
> > run_name, I get the following error:
> >
> > relax> relax_data.delete(run_name, 'R1', '500')
> > Traceback (most recent call last):
> > File "<console>", line 1, in ?
> > File "/home/h.schirra/relax_1.2.2/prompt/relax_data.py", line
> 198, in
> > delete
> > self.__relax__.specific.relax_data.delete(run=run,
> ri_label=ri_label,> frq_label=frq_label)
> > File "/home/h.schirra/relax_1.2.2/specific_fns/relax_data.py",
> line 432, in
> > delete
> > index = self.find_index(data)
> > File "/home/h.schirra/relax_1.2.2/specific_fns/relax_data.py",
> line 501, in
> > find_index
> > if self.global_flag == 1:
> > AttributeError: Rx_data instance has no attribute 'global_flag'
> >
> > ====================================
> >
> > Any ideas?
> >
> > Thanks a lot in advance!!
> >
> > Horst Joachim
> >
> >
> >
> >
> >
> >
> > _______________________________________________________
> >
> > Reply to this item at:
> >
> > <http://gna.org/bugs/?func=detailitem&item_id=6288>
> >
> > _______________________________________________
> > Message sent via/by Gna!
> > http://gna.org/
> >
> >
>
Re: [bug #6288] errors in value.copy and value.delete, possibly sequence gap related...