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
