Re: relax useRe: relax useHi Ravi,
I've noticed a peculiar message in your log file attached to your bug
report at http://gna.org/bugs/?20277. The message is at the start of
file (https://gna.org/bugs/download.php?file_id=16728) and is:
File "/Applications/relax.app/Contents/Resources/lib/python2.7/wx/_core.py",
Traceback (most recent call last):
line 16768, in <lambda>
lambda event: event.callable(*event.args, **event.kw) )
File "/Applications/relax.app/Contents/Resources/lib/python2.7/wx/_core.py",
line 13634, in SetSelection
return _core_.BookCtrlBase_SetSelection(*args, **kwargs)
TypeError: in method 'BookCtrlBase_SetSelection', expected argument 1
of type 'wxBookCtrlBase *'
Do you see this message every time you start your Mac OS X relax application?
Cheers,
Edward
On 31 October 2012 09:33, Edward d'Auvergne <edward@xxxxxxxxxxxxx> wrote:
> Hi Ravi,
>
> Would you be able to explain the problem in more detail? The error
> message you see will block you from completing an analysis. Could you
> include the output of:
>
> $ relax --info
>
> This will help me to work out what is wrong. What steps are required
> to reproduce the problem? I would recommend submitting a bug report
> to https://gna.org/bugs/?func=additem&group=relax. If you could run
> relax in logging mode with:
>
> $ relax --log ravi_failed_analysis.log --gui
>
> and then attach the log file to this bug report (please do not attach
> files to mailing list messages), I should be able to get a better
> understanding of what is happening. It is quite strange that this is
> occurring for one analysis and not another.
>
> Cheers,
>
> Edward
>
>
>
>
> On 31 October 2012 03:30, Ravi Pratap Barnwal <ravi13pb@xxxxxxxxx> wrote:
>> Hello,
>> I completed one set of run for my free protein and results are very good. Is
>> there a way to get the overall correlation time for my protein. Apart from
>> this, i was trying to run the relax for my complex but relax has started
>> giving me errors like this,
>> *******************************************
>> Exception raised in thread.
>>
>> Traceback (most recent call last):
>> File "gui/analyses/execute.pyc", line 87, in run
>> File "gui/analyses/auto_model_free.pyc", line 808, in run_analysis
>> File "auto_analyses/dauvergne_protocol.pyc", line 234, in __init__
>> File "auto_analyses/dauvergne_protocol.pyc", line 561, in execute
>> File "auto_analyses/dauvergne_protocol.pyc", line 768, in model_selection
>> File "prompt/uf_objects.pyc", line 219, in __call__
>> File "generic_fns/model_selection.pyc", line 314, in select
>> File "generic_fns/pipes.pyc", line 67, in bundle
>> File "generic_fns/pipes.pyc", line 466, in test
>> RelaxNoPipeError: RelaxError: The data pipe 'aic - mf (Tue Oct 30 18:02:41
>> 2012)' has not been created yet.
>>
>>
>> What could be doing wrong with it? I am using data from two different
>> fields.
>>
>>
>> regards
>> ravi
>>
>>
>> On Thu, Oct 25, 2012 at 7:19 AM, Edward d'Auvergne <edward@xxxxxxxxxxxxx>
>> wrote:
>>>
>>> Hi Ravi,
>>>
>>> I will answer your questions below:
>>>
>>> > (1) I am running this program on macpro computer with i7 processor and 4
>>> > Gb
>>> > run. When the program is running in GUI mode, it slows down the
>>> > computer. is
>>> > it normal or is there a way to make it faster without slowing down the
>>> > computer?
>>>
>>> A full model-free analysis - i.e. execution of the full protocol and
>>> not simply running the basic model-free models - can require a long
>>> time to calculate. This is explained in a few places in the relax
>>> manual, for example:
>>>
>>>
>>> http://www.nmr-relax.com/manual/d_Auvergne_protocol_script_mode_execution.html
>>>
>>> and:
>>>
>>> http://www.nmr-relax.com/manual/new_protocol_in_GUI.html
>>>
>>> Essentially this is a long calculation which can take up to a couple
>>> of weeks to complete, depending on the system, and you can use Gary
>>> Thompson's multi-processor code to speed things up if you need
>>> (http://www.nmr-relax.com/manual/multi_processor_framework.html).
>>>
>>> Depending on your operating system, you can use priorities to allow
>>> your computer to run at a reasonable speed during an intensive
>>> number-crunching calculation. You can renice processes using, for
>>> example, 'top' in GNU/Linux and Mac OS X systems. In MS Windows you
>>> can use the task manager to reset the priorities.
>>>
>>>
>>> > (2) My protein is 152 amino acid long. it seems the program is running
>>> > for
>>> > last few days and many more models to complete. Usually how long does it
>>> > take to complete a full automated run?
>>>
>>> As it says in the manual, this is not possible to predict but it can
>>> take up to a couple of weeks. If you are lucky, then only a few days
>>> are required. This really depends on what types of internal dynamics
>>> you have as well as the quality of the R1, R2, and NOE relaxation
>>> data. You can check the quality of the data using the Sebastien
>>> Morin's consistency testing analysis in relax
>>> (http://www.nmr-relax.com/manual/Consistency_testing.html). It might
>>> be worth running the relaxation curve-fitting and NOE calculation
>>> through relax as well to be sure of the error estimates:
>>>
>>> http://www.nmr-relax.com/manual/Relaxation_curve_fitting.html
>>> http://www.nmr-relax.com/manual/Calculating_NOE.html
>>>
>>> These are simply links to the relevant chapters of the relax user
>>> manual. What software did you use to calculate your R1, R2, and NOE
>>> data? My paper:
>>>
>>> d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
>>> dynamic models II. A new methodology for the dual optimisation of the
>>> model-free parameters and the Brownian rotational diffusion tensor. J.
>>> Biomol. NMR, 40(2), 121-133.
>>> (http://dx.doi.org/10.1007/s10858-007-9213-3).
>>>
>>> talks about this as well. See figure 2 for an idea of how long global
>>> convergence of the combined model-free optimisation and model-free
>>> model selection problem can take.
>>>
>>>
>>> > (3) what are differences between local_tm models and model-free models?
>>> > What
>>> > i could see is that local-tm models have tm with it whereas model-free
>>> > models dont!
>>>
>>> This is again described in the manual:
>>>
>>> http://www.nmr-relax.com/manual/model_free_models.html
>>>
>>> However a much better description is given in some of my published papers:
>>>
>>> d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of the
>>> model-free problem and the diffusion seeded model-free paradigm. Mol.
>>> Biosyst., 3(7), 483-494. (http://dx.doi.org/10.1039/b702202f).
>>>
>>> and:
>>>
>>> d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
>>> dynamic models II. A new methodology for the dual optimisation of the
>>> model-free parameters and the Brownian rotational diffusion tensor. J.
>>> Biomol. NMR, 40(2), 121-133.
>>> (http://dx.doi.org/10.1007/s10858-007-9213-3).
>>>
>>> Note that these papers also describe the protocol that you are using.
>>> The Lipari-Szabo model-free theory is only part of the problem. On
>>> top of this is the bigger problem of the internal bond motions verses
>>> external global tumbling. A number of protocols have been developed
>>> over time to solve this problem (see the manual and the above papers
>>> for a list of these protocols), and in relax via the GUI you are using
>>> the new model-free protocol that I developed in the group of Prof.
>>> Paul Gooley. You can click on the 'About' button in the GUI for more
>>> information.
>>>
>>>
>>> > (4) I want to see the results of local_tm run which seems to be over
>>> > with
>>> > aic and tm0-tm9 folders created having results.bz2 in it? How to check
>>> > the
>>> > results, for example, i want to see the overall correlation time of my
>>> > protein, how to see the results.bz2 file and which folder to check? How
>>> > to
>>> > look for other parameters?
>>>
>>> You will have to wait until the analysis is finished. To understand
>>> what is possible, you will need to minimally read the two references
>>> given above. But to properly understand the complexity of the
>>> analysis you are performing, you should really read all the relevant
>>> references listed in the citations chapter of the user manual
>>> (http://www.nmr-relax.com/manual/Citations.html, though the citations
>>> here are not properly built so you should see the PDF version of the
>>> manual http://download.gna.org/relax/manual/relax.pdf).
>>>
>>> After reading these, you will note that there is no overall
>>> correlation time for the local tm models - and this is the power of
>>> these models and the key to the start of the protocol I developed.
>>> You will also see that you need to wait until the protocol has
>>> completed to obtain the information that you are after. Until then
>>> relax will not be responsive and you will not be able to do anything.
>>> I would also recommend looking at Figure 1 of my 2008b paper.
>>>
>>>
>>> > Since, i am trying use relax for 1st time, these questions might be
>>> > naive of
>>> > its kind. Sorry for any inconvenience and looking forward to hear from
>>> > your
>>> > side.
>>>
>>> This isn't a problem. If you have any other questions or need
>>> pointers to the right documentation, user manual section or reference,
>>> don't hesitate to ask.
>>>
>>> Regards,
>>>
>>> Edward
>>
>>
>>
>>