Hi Ravi, I have now created a fix for the bug you reported at https://gna.org/bugs/?20277. This fix is in the relax source code repository (http://article.gmane.org/gmane.science.nmr.relax.scm/15700). If you wish, you can obtain the latest code as described in the open source infrastructure chapter of the user manual (http://www.nmr-relax.com/manual/Open_source_infrastructure.html). However the change is quite trivial and essentially stops you from moving past the first grid search. Therefore you don't really need the new code to solve this issue.
The problem is that, for some reason, no spins are selected by the time you reach the optimisation stage. I would recommend you follow the tutorial in the relax manual exactly to try to find the source of this problem (http://www.nmr-relax.com/manual/new_protocol_in_GUI.html). The messages in the file attached to the bug report are also incomplete. Therefore I would recommend starting from scratch rather than from a saved state, as I'm sure there is an earlier RelaxWarning that will tell you exactly what the problem is. I hope this helps. Regards, Edward On 31 October 2012 16:33, 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 >>> >>> >>> >>> _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
