Re: relax-users@gna.org
Hi Venkat, This is clearly a wxPython issue, as you can run relax in the prompt/script modes but not GUI mode. I remember you have previously had wxPython issues: http://thread.gmane.org/gmane.science.nmr.relax.user/1247 Have you changed anything since then? The version appears to be identical. Your wxPython is horribly broken on Centos 5 and there is not much I can do about that. How was this installed? Was it self compiled on your Centos 6 machine? It appears pretty obvious that your current wxPython binaries are incompatible with the libraries installed on your Centos 5 machine. You may need to have separate wxPython installations for Centos 5 and 6 (possibly then also separate Python installations). As I suggested in that old thread, maybe you could try and see if the wx demos run on Centos 5. Unfortunately as this is not part of relax, there is not too much I can do to help you. If your sys admin cannot solve this, there is a fix. You can download the Python, numpy, scipy, and wxPython sources and compile these into your home directory using: $ configure --prefix=~ Or place them into a special directory. For example to test relax, I have a special directory called /data/python/. I have compiled Python versions 1.0, 1.5, 1.6, 2.0, 2.1, 2.2, 2.3, 2.4, 2.5, 2.6, 2.7, 3.0, 3.1, 3.2, and 3.3 using the configure script option '--prefix=/data/python/'. Each of these have numpy, scipy, and wxPython compiled for them, when possible. This is using, for example: $ /data/python/python1.5 setup.py install I can then test relax with the 'devel_scripts/python_multiversion_test_suite.py' script pointing to all these Python versions. Note that this is completely performed as a user - at no point was root access required (though you many need the admin to install some development packages if missing). If your home directory is shared, then maybe you can have separate directories for a Centos 5 and Centos 6 build. I hope some of this info helps. Regards, Edward On 6 February 2013 18:20, Venkat V ven...@hkl.hms.harvard.edu wrote: Hi Martin, relax --info gives me this. So wx-Python is 2.8.12.1 version. We have the same central python setup running on both centos 5 and centos 6. relax GUI works on centos 6 but not on centos 5 (this is true whether the machine is x86 or x86_64). minfx True Unknown bmrblibTrue Unknown numpy True 1.6.1 scipy True 0.10.0 wxPython True 2.8.12.1 (gtk2-unicode) mpi4py False epydoc False optparse True 1.5.3 readline True profileTrue bz2True gzip True io True os.devnull True xmlTrue 0.8.4 (internal) Venkat On Wed, Feb 6, 2013 at 10:32 PM, Martin Ballaschk ballas...@fmp-berlin.de wrote: Hi Venkat, did you try to update wxPython, the GUI framework that relax relies on? This gave me a lot of headaches on the Mac when I first tried relax and is still in heavy development, IIRC. Edward certainly can elaborate on that, but maybe it's a good idea to check if your system meets all the dependencies that are listed on the relax website, especially if you have a up-to-date wxPython version: • Python = 2.3: Python-2.7.3.tar.bz2 • NumPy = 1.0.4: NumPy downloads • SciPy (optional) = 0.7.1: SciPy downloads • wxPython (optional) = 2.8: wxPython stable downloads http://www.nmr-relax.com/download.html#Current_release Regards Martin On 06.02.2013, at 17:43, Venkat V ven...@hkl.hms.harvard.edu wrote: Hi, I had installed both relax 2.2.0 and 2.2.1 on i386 and x86_64 linux machines. The command line runs OK on all machines. The GUI fails with seg fault on centos 5 machines (both i386 and x86_6). The GUI works OK on centos 6 machines ( both i386 and x86_64). The python version is 2.7.2. Venkat ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org 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 -- Martin Ballaschk AG Schmieder Leibniz-Institut für Molekulare Pharmakologie Robert-Rössle-Str. 10 13125 Berlin ballas...@fmp-berlin.de Tel.: +49-30-94793-234/315 Büro: A 1.26 Labor: C 1.10 ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org 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
Re: m0 models
Hi, As you are working with complexes, then maybe an issue is that a single diffusion tensor is not an adequate representation of the system, resulting in the model m0 appearing more than it should. This might be the case if the complex is not tight and you have a mixture of complex and free monomers. This has been looked at in Schurr et al, 1994, but no one has come up with a solution to this problem for model-free analysis. Maybe you could be the first ;) I'm not done with the analysis of all of my complexes, but I fear that even with everything done correctly there will be m0 all over the place and I don't know how to interpret this in terms of mobility. Judging from the runs I did until now, especially the interesting (i.e. probably more mobile) regions of the more interesting protein show this behaviour. As I said, I have quite large areas that disappear from my spectra from one protein variant to the other – so this is an indication for exchange mobility in this regions which is interesting for itself! Neighbouring regions have a lot of m0 (in 62 of ~220 assigned residues minus 28 unresolved) and in the ellipsoidal diffusion model there is also a lot of strange Rex = 0. terms, the other models show Rex of around 10^-18 (=nearly zero). Convergence is reached in 20-30 rounds for each diffusion model, no oscillations are visible. Is this Rex in the results file or in the extracted version? Note that relax stores Rex internally as the field strength independent value of: sigma_ex = Rex / omega**2 Hence the value in the relax state files will be on the order of 'super tiny'. You need to multiply omega_N squared to obtain the value you would expect on a given spectrometer. Also note that currently in all model-free software, Rex is assumed to be fast and hence scales quadratically with field strength - this might be another source of problems for your analysis. The current data are not perfect, as the necessary (!) R1 temperature compensation was not used yet and also no soft pulses. So obviously I have re-record some of the data. I used only one single sample, which was pretty stable over the time I measured (no visible precipitation, but very slight decreasing TROSY intensity). The temperature is off by less than 1 K (remember our fucked-up but-now-apparently-fixed calibration procedure). The consistency tests returned a fairly centered distribution (ratio of j0 at different fields: 0.993 +/- 0.174) of moderate consistency (j0 test (field1-field2)/field2 = 0.08). R1 temperature compensation is generally not needed as it is quite a cold experiment, hence will almost always match the normal spectrometer calibration. But single scan interleaving is a good idea to average changes which occur during the experiment (for example day and night temperature fluctuations which always occur to some extent). Everything else seems fine. That said, I don't see so overwhelmingly much of these stark m0 effects in the protein I expect to be more rigid, although I have only a dataset wich is highly inconsistent due to large temperature diffences, that was much less stable used only old-school experiments with hard pulses have been used. m0 almost never appears for rigid, well behaved proteins as the dynamics is easy to extract. The m0 is a sign that something or some process is hiding the dynamics in the relation data. I.e. the single diffusion tensor with internal model-free compatible motions is not adequate. Or that the data for a spin is too noisy because your system is so big. My SH3 testing data don't show this kind of behaviour (no m0 at all), but these have incredibly fat signal. Having a real protein changes a few things I guess, especially in terms of S/N. If m0 appears in SH3, I would be worried. In a real protein though, the data for some residues can be rubbish, hence m0 is very valid as the dynamics data is no longer present. m0 then tells you that you have 4 grey pixels ;) Maybe it's because of more complex motions. Maybe I should have gone for relaxation dispersion in the first place. But one step after another seemed reasonable at that time. (I'm currently quite desperately looking for an introductory review like Séb Morin's practical guide for relaxation dispersion – do you know one?) Relaxation dispersion might be interesting, but from what you describe I don't think dispersion data will tell you much other than what you already see with weak peaks. Actually, as your system is 45 kDa, I would not expect that you would see much dispersion at all - your weak peaks are due to protein size and not Rex. As for a guide about relaxation dispersion, I know no equivalent to Seb's guide. There are some reviews from the Art Palmer and Lewis Kay groups which could be useful. If you do find something, I'd be interested to have the reference. Maybe this relates to model m9 in relax. Sometimes the very weak
