Hello, I dont see this error when i start he relax. I do solved the problem. It seems some formatting error associated with the R1/R2 and noe files, was a culprit.
Also, when i was checking my results from the previous run, i noticed relax did not run "prolate spheroid" and "oblate spheroid" modes. It did create a final folder with all the files. Also, the correlation time given by relax seems to be double of what we got from model-free, how can this be possible? It was based on sphere mode. regards ravi On Wed, Oct 31, 2012 at 8:33 AM, Edward d'Auvergne <[email protected]>wrote: > Hi 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: > > Traceback (most recent call last): > File > "/Applications/relax.app/Contents/Resources/lib/python2.7/wx/_core.py", > 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 <[email protected]> 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 <[email protected]> > 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 < > [email protected]> > >> 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 > >> > >> > >> > >> >
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