Re: [bug #6288] errors in value.copy and value.delete, possibly sequence gap related... -- July 07, 2006 - 10:22

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>
>
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