Hi Edward,
I have a question that's an extension of Ravi's.
I'm using my laptop to run relax and I'd like to be able to halt the
calculation and then return to it later to avoid leaving my computer on the
entire time. If I remember correctly, it was possible for me to do this when
running relax from the command line. However, when I stop and start the
calculation in the GUI it always returns to the beginning of the
calculation. Furthermore, while the calculation is running, the "save" and
"save as" buttons are shaded out. I reviewed the mailing lists but couldn't
see this brought up anywhere.
I'm running relax 2.1.2 on lion, although I've also noted this issue on
earlier versions of relax.
Regards,
Ian
On 2012-10-25, at 3:19 PM, Edward d'Auvergne 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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Re: relax use