Hi, You should have a look at the paper of Schurr, 1994. It should be easy enough to find. Though I have it listed in my PhD thesis if it is a problem to find (see http://www.nmr-relax.com/refs.html). He had a look at monomer-dimer mixtures using synthetic test systems. It is the most comprehensive reference for this issue, and it describes the likely artifacts. You should know these, so that you don't accidentally make false conclusions about the dynamics.
Regards, Edward On 24 February 2011 12:08, Maddy Strickland <[email protected]> wrote: > Thanks Seb and Edward, > > The off rate is 13.8*10^-3 s-1, on rate is 5.3*10^6 M-1s-1. It's been > developed to be a good binder (Kd=2.6 nm) - does that seem alright? I > suppose we won't know until we look at the data - we have access to two > fields - 600 and 900, which we'll use for free and bound forms. Hopefully > it should bind strongly enough. If not, we're looking for stronger > binders anyway, so we could use one of those when it comes along. > > Thanks > > Maddy > > ---------------------------- Original Message ---------------------------- > Subject: relax-users Digest, Vol 56, Issue 4 > From: [email protected] > Date: Thu, February 24, 2011 10:53 am > To: [email protected] > -------------------------------------------------------------------------- > > Send relax-users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.gna.org/listinfo/relax-users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of relax-users digest..." > > > Today's Topics: > > 1. Binding studies (Maddy Strickland) > 2. Re: ImporError (Edward d'Auvergne) > 3. Re: Binding studies (Edward d'Auvergne) > 4. Re: Binding studies (S?bastien Morin) > 5. Re: ImporError (Edward d'Auvergne) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 23 Feb 2011 10:04:24 -0000 (GMT) > From: "Maddy Strickland" <[email protected]> > Subject: Binding studies > To: [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain;charset=iso-8859-15 > > Hi everyone, > > I'm moving on to looking at dynamics of binding to a receptor which I've > already studied using Relax for Lipari-Szabo data. I was wondering if I > added some unlabelled peptide to the 15n receptor how I could study the > new relaxation data? Can I still use Relax and the same pulse sequences > etc. or do I need a program specific to binding? It's a fairly strong > binder, but it would render the receptor more of a cylinder than a > sphere... What do you all think? > > > Madeleine Strickland > > > > > > ------------------------------ > > Message: 2 > Date: Thu, 24 Feb 2011 10:11:42 +0100 > From: "Edward d'Auvergne" <[email protected]> > Subject: Re: ImporError > To: Min-Kyu Cho <[email protected]> > Cc: [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=EUC-KR > > Hi, > > This is very puzzling :S I will install Python 2.6 and make a new > distribution archive. > > Bye, > > Edward > > > On 22 February 2011 22:30, Min-Kyu Cho <[email protected]> wrote: >> Hi, >> >> I tried and got this error; >> >> >> relax 1.3.10 >> >> Molecular dynamics by NMR data analysis >> >> Copyright (C) 2001-2006 Edward d'Auvergne >> Copyright (C) 2006-2011 the relax development team >> >> This is free software which you are welcome to modify and redistribute > under the >> conditions of the GNU General Public License (GPL). This program, > including all >> modules, is licensed under the GPL and comes with absolutely no > warranty. For >> details type 'GPL' within the relax prompt. >> >> Assistance in using the relax prompt and scripting interface can be > accessed by >> typing 'help' within the prompt. >> >> ImportError: DLL load failed: ??? ??? ?? ? ????. (= Cannot find the > specified module). >> Relaxation curve fitting is unavailable, try compiling the C modules. >> >> relax> from maths_fns.realx_fit import setup >> Traceback (most recent call last): >> File "<console>", line 1, in <module> >> ImportError: No module named realx_fit >> >> ------------------------------------ >> But with ' from maths_fns.realx_fit import setup', now I got the same > error you showed me previously. >> >> Regards, >> Min-Kyu >> >> +------------------------------+ >> Cho, Min-Kyu >> Rm. 5110D MRBIII, 465 21st Ave S. >> Vanderbilt University School of Medicine, Nashville, TN 37232-8725 >> Phone: 615-936-3757 / Fax: 615-936-2211 >> >> >> | > -----Original Message----- >> | > From: [email protected] [mailto:[email protected]] On >> | > Behalf Of Edward d'Auvergne >> | > Sent: Tuesday, February 22, 2011 2:58 PM >> | > To: Cho, Min-Kyu >> | > Cc: [email protected] >> | > Subject: Re: ImporError >> | > >> | > Hi, >> | > >> | > I've updated to Python 2.7.1 and numpy 1.5.1 on my 32-bit Windows >> | > building environment and made a new distribution archive for relax >> | > 1.3.10. You can find it at the relax download location: >> | > >> | > http://download.gna.org/relax/ >> | > >> | > The file is called relax-1.3.10.Win32.py27.zip. Hopefully this one >> | > works! >> | > >> | > Regards, >> | > >> | > Edward >> | > >> | > >> | > >> | > 2011/2/22 Edward d'Auvergne <[email protected]>: >> | > > Hi, >> | > > >> | > > This message is actually a little different. The DLL load failed >> | > > message means that the file (maths_fns/relax_fit.dll) exists but it >> | > > cannot be loaded. In the message I gave, the file does not exist. >> | > > Unfortunately the message is not too informative, so I can't work out >> | > > if it is a Windows problem or a software version problem. I compiled >> | > > this in a virtual machine. It was Windows 2000 (a very old 32-bit >> | > > system, but should still produce things that run on all windows >> | > > versions), with Python 2.5 and numpy 1.1. It could be that the numpy >> | > > versions are too different, mine is too old and yours is too new. It >> | > > could also be the Windows version not being able to run old Windows >> | > > software. If it is the numpy problem, I might try to solve that for >> | > > the next version of relax. If it is the Windows version problem, >> | > > unfortunately there is really nothing I can do about that. >> | > > >> | > > If this is your own computer and you have administrator access, an >> | > > option is to try to install scons and MS Visual C++ >> | > > (http://www.nmr-relax.com/windows_devel.html). Otherwise you could >> | > > wait until the next relax version to see. Actually, maybe I'll > try to >> | > > upgrade Python and numpy on my Windows building system and make a new >> | > > zip file for you to test. >> | > > >> | > > Regards, >> | > > >> | > > Edward >> | > > >> | > > >> | > > On 22 February 2011 18:42, Min-Kyu Cho <[email protected]> >> | > wrote: >> | > >> Yes, I got the same error message. >> | > >> >> | > >> Traceback (most recent call last): >> | > >> File "<console>", line 1, in <module> >> | > >> ImportError: DLL load failed: ??? ??? ?? ? ????. ==> In Korean, >> | > "Cannot find the module". >> | > >> >> | > >> Regards, >> | > >> Min-Kyu >> | > >> >> | > >> +------------------------------+ >> | > >> Cho, Min-Kyu >> | > >> Rm. 5110D MRBIII, 465 21st Ave S. >> | > >> Vanderbilt University School of Medicine, Nashville, TN 37232-8725 >> | > >> Phone: 615-936-3757 / Fax: 615-936-2211 >> | > >> >> | > >> >> | > >> | > -----Original Message----- >> | > >> | > From: [email protected] >> | > [mailto:[email protected]] On >> | > >> | > Behalf Of Edward d'Auvergne >> | > >> | > Sent: Tuesday, February 22, 2011 10:45 AM >> | > >> | > To: Cho, Min-Kyu >> | > >> | > Cc: [email protected] >> | > >> | > Subject: Re: ImporError >> | > >> | > >> | > >> | > Hi, >> | > >> | > >> | > >> | > This is quite strange! The Win32 distribution should have >> | > worked :S >> | > >> | > Are you sure it was this version? What happens if you type: >> | > >> | > >> | > >> | > relax> from maths_fns.relax_fit import setup >> | > >> | > >> | > >> | > Do you get something like: >> | > >> | > >> | > >> | > relax> from maths_fns.relax_fit import setup >> | > >> | > Traceback (most recent call last): >> | > >> | > File "<console>", line 1, in <module> >> | > >> | > ImportError: No module named relax_fit >> | > >> | > relax> >> | > >> | > >> | > >> | > Hmmm, what is Windows doing here :S >> | > >> | > >> | > >> | > Bye, >> | > >> | > >> | > >> | > Edward >> | > >> | > >> | > >> | > >> | > >> | > >> | > >> | > On 22 February 2011 17:18, Min-Kyu Cho <min- >> | > [email protected]> >> | > >> | > wrote: >> | > >> | > > Hi, >> | > >> | > > >> | > >> | > > Here is the output with >> relax --help: >> | > >> | > > >> | > >> | > > relax 1.3.10 >> | > >> | > > >> | > >> | > > Molecular dynamics by NMR data analysis >> | > >> | > > >> | > >> | > > Copyright (C) 2001-2006 Edward d'Auvergne >> | > >> | > > Copyright (C) 2006-2011 the relax development > team >> | > >> | > > >> | > >> | > > This is free software which you are welcome to modify and >> | > redistribute >> | > >> | > under >> | > >> | > > the >> | > >> | > > conditions of the GNU General Public License (GPL). This >> | > program, >> | > >> | > including >> | > >> | > > all >> | > >> | > > modules, is licensed under the GPL and comes with > absolutely no >> | > >> | > warranty. >> | > >> | > > For >> | > >> | > > details type 'GPL' within the relax prompt. >> | > >> | > > >> | > >> | > > Assistance in using the relax prompt and scripting interface >> | > can be >> | > >> | > accessed >> | > >> | > > by >> | > >> | > > typing 'help' within the prompt. >> | > >> | > > >> | > >> | > > ImportError: relaxation curve fitting is unavailable, the >> | > >> | > corresponding C >> | > >> | > > modules have not been compiled. >> | > >> | > > >> | > >> | > > Hardware information: >> | > >> | > > Machine: x86 >> | > >> | > > Processor: x86 Family 6 Model 23 Stepping 6, >> | > >> | > GenuineIntel >> | > >> | > > >> | > >> | > > System information: >> | > >> | > > System: Windows >> | > >> | > > Release: post2008Server >> | > >> | > > Version: 6.1.7600 >> | > >> | > > Win32 version: post2008Server 6.1.7600 > Multiprocessor >> | > Free >> | > >> | > > Distribution: >> | > >> | > > Full platform string: Windows-post2008Server-6.1.7600 >> | > >> | > > >> | > >> | > > Software information: >> | > >> | > > Architecture: 32bit WindowsPE >> | > >> | > > Python version: 2.6.5 >> | > >> | > > Python branch: tags/r265 >> | > >> | > > Python build: r265:79096, Mar 19 2010 21:48:26 >> | > >> | > > Python compiler: MSC v.1500 32 bit (Intel) >> | > >> | > > Python implementation: CPython >> | > >> | > > Python revision: 79096 >> | > >> | > > Numpy version: 1.5.1 >> | > >> | > > Libc version: >> | > >> | > > >> | > >> | > > Python packages (most are optional): >> | > >> | > > >> | > >> | > > Package Installed Version Path >> | > >> | > > >> | > >> | > minfx True Unknown >> | > D:\Programs\relax\minfx >> | > >> | > > bmrblib False >> | > >> | > > numpy True 1.5.1 > C:\Program >> | > >> | > > Files\Python26\lib\site-packages\numpy >> | > >> | > > ScientificPython False >> | > >> | > > wxPython True >> | > >> | > > mpi4py False >> | > >> | > > epydoc False >> | > >> | > > optparse True 1.5.3 > C:\Program >> | > >> | > > Files\Python26\lib\optparse.py >> | > >> | > > Numeric False >> | > >> | > > readline True > C:\Program >> | > >> | > > Files\Python26\lib\site-packages\readline.py >> | > >> | > > profile True > C:\Program >> | > >> | > > Files\Python26\lib\profile.py >> | > >> | > > bz2 True > C:\Program >> | > >> | > > Files\Python26\DLLs\bz2.pyd >> | > >> | > > gzip True > C:\Program >> | > >> | > > Files\Python26\lib\gzip.py >> | > >> | > > os.devnull True > C:\Program >> | > >> | > > Files\Python26\lib\os.pyc >> | > >> | > > >> | > >> | > > Compiled relax C modules: >> | > >> | > > Relaxation curve fitting: False >> | > >> | > > --- >> | > >> | > > >> | > >> | > > It is clear that I don't have C library. At the moment, I > don't >> | > need >> | > >> | > it, but >> | > >> | > > will try later with my data. >> | > >> | > > >> | > >> | > > Regards, >> | > >> | > > Min-Kyu >> | > >> | > > >> | > >> | > > >> | > >> | > > +------------------------------+ >> | > >> | > > Cho, Min-Kyu >> | > >> | > > Rm. 5110D MRBIII, 465 21st Ave S. >> | > >> | > > Vanderbilt University School of Medicine, Nashville, TN 37232- >> | > 8725 >> | > >> | > > Phone: 615-936-3757 / Fax: 615-936-2211 >> | > >> | > > >> | > >> | > > | > -----Original Message----- >> | > >> | > > | > From: [email protected] >> | > >> | > [mailto:[email protected]] On >> | > >> | > > | > Behalf Of Edward d'Auvergne >> | > >> | > > | > Sent: Tuesday, February 22, 2011 3:21 AM >> | > >> | > > | > To: Cho, Min-Kyu >> | > >> | > > | > Cc: [email protected] >> | > >> | > > | > Subject: Re: ImporError >> | > >> | > > | > >> | > >> | > > | > Hi, >> | > >> | > > | > >> | > >> | > > | > Are you using the Win32 compiled version from >> | > >> | > > | > http://www.nmr-relax.com/download.html? Could you run: >> | > >> | > > | > >> | > >> | > > | > $ relax --info >> | > >> | > > | > >> | > >> | > > | > and copy the result? The problem here is that the C >> | > modules for >> | > >> | > the >> | > >> | > > | > relaxation curve-fitting of the R1 and R2 rates is either >> | > not >> | > >> | > compiled >> | > >> | > > | > or the compiled version is incompatible with your >> | > combination of >> | > >> | > MS >> | > >> | > > | > Windows version, Python version, and numpy version. It > may >> | > be >> | > >> | > that >> | > >> | > > | > you are using a 64-bit version of Windows, in which case >> | > the 32- >> | > >> | > bit C >> | > >> | > > | > module will not work. If you don't need to use this part >> | > of relax, >> | > >> | > > | > you can safely ignore this warning. >> | > >> | > > | > >> | > >> | > > | > However, if you do need it and you are brave, I have >> | > created >> | > >> | > > | > instructions on how to set up a development environment on >> | > Windows >> | > >> | > to >> | > >> | > > | > allow the C modules to be compiled: >> | > >> | > > | > >> | > >> | > > | > http://www.nmr-relax.com/windows_devel.html >> | > >> | > > | > >> | > >> | > > | > With scons and MS Visual C++ installed, it should be >> | > possible to >> | > >> | > > | > compile the module. >> | > >> | > > | > >> | > >> | > > | > Regards, >> | > >> | > > | > >> | > >> | > > | > Edward >> | > >> | > > | > >> | > >> | > > | > >> | > >> | > > | > >> | > >> | > > | > >> | > >> | > > | > On 22 February 2011 06:13, Min-Kyu Cho <min- >> | > >> | > [email protected]> >> | > >> | > > | > wrote: >> | > >> | > > | > > Hi Eddy, >> | > >> | > > | > > >> | > >> | > > | > > >> | > >> | > > | > > >> | > >> | > > | > > I got the following error when I executed 'relax' on >> | > Window7; >> | > >> | > > | > > >> | > >> | > > | > > >> | > >> | > > | > > >> | > >> | > > | > > ImportError: relaxation curve fitting is unavailable, > the >> | > >> | > > | > corresponding C >> | > >> | > > | > > module have not been compiled. >> | > >> | > > | > > >> | > >> | > > | > > >> | > >> | > > | > > >> | > >> | > > | > > What should I do? >> | > >> | > > | > > >> | > >> | > > | > > >> | > >> | > > | > > >> | > >> | > > | > > Cheers, >> | > >> | > > | > > >> | > >> | > > | > > Min-Kyu >> | > >> | > > | > > >> | > >> | > > | > > >> | > >> | > > | > > >> | > >> | > > | > > _______________________________________________ >> | > >> | > > | > > relax (http://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 >> | > >> | > > | > > >> | > >> | > > | > > >> | > >> | > > >> | > >> | > > >> | > >> | > > _______________________________________________ >> | > >> | > > relax (http://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 >> | > >> | > > >> | > >> >> | > >> >> | > > >> >> >> _______________________________________________ >> relax (http://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 >> > > > > ------------------------------ > > Message: 3 > Date: Thu, 24 Feb 2011 10:45:39 +0100 > From: "Edward d'Auvergne" <[email protected]> > Subject: Re: Binding studies > To: Maddy Strickland <[email protected]> > Cc: [email protected], S?bastien M <[email protected]> > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > This can be tricky. Can you estimate the percentage of monomer verses > dimer? Can you also estimate the amount of time the peptide binds to > the receptor? Do you have binding data for the NMR sample conditions? > If the more than 90% of the receptor is bound to the peptide and the > time bound to the receptor is significant, then you should be able to > handle this with standard model-free analysis using a single diffusion > tensor. This will likely require data at 2 or more field strengths. > Seb, have you worked with this situation? > > Regards, > > Edward > > > On 23 February 2011 11:04, Maddy Strickland <[email protected]> > wrote: >> Hi everyone, >> >> I'm moving on to looking at dynamics of binding to a receptor which I've >> already studied using Relax for Lipari-Szabo data. ?I was wondering if I >> added some unlabelled peptide to the 15n receptor how I could study the >> new relaxation data? ?Can I still use Relax and the same pulse sequences >> etc. or do I need a program specific to binding? ?It's a fairly strong >> binder, but it would render the receptor more of a cylinder than a >> sphere... ?What do you all think? >> >> >> Madeleine Strickland >> >> >> >> _______________________________________________ >> relax (http://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 >> > > > > ------------------------------ > > Message: 4 > Date: Thu, 24 Feb 2011 11:13:41 +0100 > From: S?bastien Morin <[email protected]> > Subject: Re: Binding studies > To: Edward d'Auvergne <[email protected]> > Cc: Maddy Strickland <[email protected]>, > "[email protected]" <[email protected]>, S?bastien M > <[email protected]> > Message-ID: <[email protected]> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, > > I have not worked with this situation. > > However, I agree that binding kinetics should be known (on and off > rates) and a majority of bound complex should exist over time, otherwise > the situation might be tricky since some contribution from unbound > protein might arise (with a shorter correlation time, and potentially > different dynamics). Also, contribution from potential conformational > exchange caused by binding and unbinding of the ligand (depending on the > exchange rate, i.e. on and off rates), rather than 'real' changes in > dynamics on the protein, could complicate analysis and give a false > impression of changes in the protein dynamics. > > I hope this helps. > > Best regards, > > > S?b :) > > > On 11-02-24 10:45 AM, Edward d'Auvergne wrote: >> Hi, >> >> This can be tricky. Can you estimate the percentage of monomer verses >> dimer? Can you also estimate the amount of time the peptide binds to >> the receptor? Do you have binding data for the NMR sample conditions? >> If the more than 90% of the receptor is bound to the peptide and the >> time bound to the receptor is significant, then you should be able to >> handle this with standard model-free analysis using a single diffusion >> tensor. This will likely require data at 2 or more field strengths. >> Seb, have you worked with this situation? >> >> Regards, >> >> Edward >> >> >> On 23 February 2011 11:04, Maddy Strickland<[email protected]> > wrote: >>> Hi everyone, >>> >>> I'm moving on to looking at dynamics of binding to a receptor which I've >>> already studied using Relax for Lipari-Szabo data. I was wondering if I >>> added some unlabelled peptide to the 15n receptor how I could study the >>> new relaxation data? Can I still use Relax and the same pulse sequences >>> etc. or do I need a program specific to binding? It's a fairly strong >>> binder, but it would render the receptor more of a cylinder than a >>> sphere... What do you all think? >>> >>> >>> Madeleine Strickland >>> >>> >>> >>> _______________________________________________ >>> relax (http://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 >>> > > -- > S?bastien Morin, Ph.D. > Postdoctoral fellow > S. Grzesiek NMR Laboratory > Biozentrum, Universit?t Basel > Basel, Switzerland > > > > > ------------------------------ > > Message: 5 > Date: Thu, 24 Feb 2011 11:53:14 +0100 > From: "Edward d'Auvergne" <[email protected]> > Subject: Re: ImporError > To: Min-Kyu Cho <[email protected]> > Cc: [email protected] > Message-ID: > <[email protected]> > Content-Type: text/plain; charset=EUC-KR > > Hi, > > I've now build the C modules using Python 2.6.6 with numpy 1.5.1, on > MS Windows 2000. The file is called relax-1.3.10.Win32.py26.zip and > you can find it at http://download.gna.org/relax. Could you test this > one out? > > Cheers, > > Edward > > > 2011/2/24 Edward d'Auvergne <[email protected]>: >> Hi, >> >> This is very puzzling :S I will install Python 2.6 and make a new >> distribution archive. >> >> Bye, >> >> Edward >> >> >> On 22 February 2011 22:30, Min-Kyu Cho <[email protected]> wrote: >>> Hi, >>> >>> I tried and got this error; >>> >>> >>> relax 1.3.10 >>> >>> Molecular dynamics by NMR data analysis >>> >>> Copyright (C) 2001-2006 Edward d'Auvergne >>> Copyright (C) 2006-2011 the relax development team >>> >>> This is free software which you are welcome to modify and redistribute > under the >>> conditions of the GNU General Public License (GPL). This program, > including all >>> modules, is licensed under the GPL and comes with absolutely no > warranty. For >>> details type 'GPL' within the relax prompt. >>> >>> Assistance in using the relax prompt and scripting interface can be > accessed by >>> typing 'help' within the prompt. >>> >>> ImportError: DLL load failed: ??? ??? ?? ? ????. (= Cannot find the > specified module). >>> Relaxation curve fitting is unavailable, try compiling the C modules. >>> >>> relax> from maths_fns.realx_fit import setup >>> Traceback (most recent call last): >>> File "<console>", line 1, in <module> >>> ImportError: No module named realx_fit >>> >>> ------------------------------------ >>> But with ' from maths_fns.realx_fit import setup', now I got the same > error you showed me previously. >>> >>> Regards, >>> Min-Kyu >>> >>> +------------------------------+ >>> Cho, Min-Kyu >>> Rm. 5110D MRBIII, 465 21st Ave S. >>> Vanderbilt University School of Medicine, Nashville, TN 37232-8725 >>> Phone: 615-936-3757 / Fax: 615-936-2211 >>> >>> >>> | > -----Original Message----- >>> | > From: [email protected] > [mailto:[email protected]] On >>> | > Behalf Of Edward d'Auvergne >>> | > Sent: Tuesday, February 22, 2011 2:58 PM >>> | > To: Cho, Min-Kyu >>> | > Cc: [email protected] >>> | > Subject: Re: ImporError >>> | > >>> | > Hi, >>> | > >>> | > I've updated to Python 2.7.1 and numpy 1.5.1 on my 32-bit Windows >>> | > building environment and made a new distribution archive for relax >>> | > 1.3.10. You can find it at the relax download location: >>> | > >>> | > http://download.gna.org/relax/ >>> | > >>> | > The file is called relax-1.3.10.Win32.py27.zip. Hopefully this one >>> | > works! >>> | > >>> | > Regards, >>> | > >>> | > Edward >>> | > >>> | > >>> | > >>> | > 2011/2/22 Edward d'Auvergne <[email protected]>: >>> | > > Hi, >>> | > > >>> | > > This message is actually a little different. The DLL load failed >>> | > > message means that the file (maths_fns/relax_fit.dll) exists but it >>> | > > cannot be loaded. In the message I gave, the file does not exist. >>> | > > Unfortunately the message is not too informative, so I can't work > out >>> | > > if it is a Windows problem or a software version problem. I > compiled >>> | > > this in a virtual machine. It was Windows 2000 (a very old 32-bit >>> | > > system, but should still produce things that run on all windows >>> | > > versions), with Python 2.5 and numpy 1.1. It could be that the > numpy >>> | > > versions are too different, mine is too old and yours is too new. > It >>> | > > could also be the Windows version not being able to run old Windows >>> | > > software. If it is the numpy problem, I might try to solve that for >>> | > > the next version of relax. If it is the Windows version problem, >>> | > > unfortunately there is really nothing I can do about that. >>> | > > >>> | > > If this is your own computer and you have administrator access, an >>> | > > option is to try to install scons and MS Visual C++ >>> | > > (http://www.nmr-relax.com/windows_devel.html). Otherwise you could >>> | > > wait until the next relax version to see. Actually, maybe I'll > try to >>> | > > upgrade Python and numpy on my Windows building system and make a > new >>> | > > zip file for you to test. >>> | > > >>> | > > Regards, >>> | > > >>> | > > Edward >>> | > > >>> | > > >>> | > > On 22 February 2011 18:42, Min-Kyu Cho <[email protected]> >>> | > wrote: >>> | > >> Yes, I got the same error message. >>> | > >> >>> | > >> Traceback (most recent call last): >>> | > >> File "<console>", line 1, in <module> >>> | > >> ImportError: DLL load failed: ??? ??? ?? ? ????. ==> In Korean, >>> | > "Cannot find the module". >>> | > >> >>> | > >> Regards, >>> | > >> Min-Kyu >>> | > >> >>> | > >> +------------------------------+ >>> | > >> Cho, Min-Kyu >>> | > >> Rm. 5110D MRBIII, 465 21st Ave S. >>> | > >> Vanderbilt University School of Medicine, Nashville, TN 37232-8725 >>> | > >> Phone: 615-936-3757 / Fax: 615-936-2211 >>> | > >> >>> | > >> >>> | > >> | > -----Original Message----- >>> | > >> | > From: [email protected] >>> | > [mailto:[email protected]] On >>> | > >> | > Behalf Of Edward d'Auvergne >>> | > >> | > Sent: Tuesday, February 22, 2011 10:45 AM >>> | > >> | > To: Cho, Min-Kyu >>> | > >> | > Cc: [email protected] >>> | > >> | > Subject: Re: ImporError >>> | > >> | > >>> | > >> | > Hi, >>> | > >> | > >>> | > >> | > This is quite strange! The Win32 distribution should have >>> | > worked :S >>> | > >> | > Are you sure it was this version? What happens if you type: >>> | > >> | > >>> | > >> | > relax> from maths_fns.relax_fit import setup >>> | > >> | > >>> | > >> | > Do you get something like: >>> | > >> | > >>> | > >> | > relax> from maths_fns.relax_fit import setup >>> | > >> | > Traceback (most recent call last): >>> | > >> | > File "<console>", line 1, in <module> >>> | > >> | > ImportError: No module named relax_fit >>> | > >> | > relax> >>> | > >> | > >>> | > >> | > Hmmm, what is Windows doing here :S >>> | > >> | > >>> | > >> | > Bye, >>> | > >> | > >>> | > >> | > Edward >>> | > >> | > >>> | > >> | > >>> | > >> | > >>> | > >> | > On 22 February 2011 17:18, Min-Kyu Cho <min- >>> | > [email protected]> >>> | > >> | > wrote: >>> | > >> | > > Hi, >>> | > >> | > > >>> | > >> | > > Here is the output with >> relax --help: >>> | > >> | > > >>> | > >> | > > relax 1.3.10 >>> | > >> | > > >>> | > >> | > > Molecular dynamics by NMR data analysis >>> | > >> | > > >>> | > >> | > > Copyright (C) 2001-2006 Edward d'Auvergne >>> | > >> | > > Copyright (C) 2006-2011 the relax > development team >>> | > >> | > > >>> | > >> | > > This is free software which you are welcome to modify and >>> | > redistribute >>> | > >> | > under >>> | > >> | > > the >>> | > >> | > > conditions of the GNU General Public License (GPL). This >>> | > program, >>> | > >> | > including >>> | > >> | > > all >>> | > >> | > > modules, is licensed under the GPL and comes with > absolutely no >>> | > >> | > warranty. >>> | > >> | > > For >>> | > >> | > > details type 'GPL' within the relax prompt. >>> | > >> | > > >>> | > >> | > > Assistance in using the relax prompt and scripting interface >>> | > can be >>> | > >> | > accessed >>> | > >> | > > by >>> | > >> | > > typing 'help' within the prompt. >>> | > >> | > > >>> | > >> | > > ImportError: relaxation curve fitting is unavailable, the >>> | > >> | > corresponding C >>> | > >> | > > modules have not been compiled. >>> | > >> | > > >>> | > >> | > > Hardware information: >>> | > >> | > > Machine: x86 >>> | > >> | > > Processor: x86 Family 6 Model 23 Stepping 6, >>> | > >> | > GenuineIntel >>> | > >> | > > >>> | > >> | > > System information: >>> | > >> | > > System: Windows >>> | > >> | > > Release: post2008Server >>> | > >> | > > Version: 6.1.7600 >>> | > >> | > > Win32 version: post2008Server 6.1.7600 > Multiprocessor >>> | > Free >>> | > >> | > > Distribution: >>> | > >> | > > Full platform string: Windows-post2008Server-6.1.7600 >>> | > >> | > > >>> | > >> | > > Software information: >>> | > >> | > > Architecture: 32bit WindowsPE >>> | > >> | > > Python version: 2.6.5 >>> | > >> | > > Python branch: tags/r265 >>> | > >> | > > Python build: r265:79096, Mar 19 2010 21:48:26 >>> | > >> | > > Python compiler: MSC v.1500 32 bit (Intel) >>> | > >> | > > Python implementation: CPython >>> | > >> | > > Python revision: 79096 >>> | > >> | > > Numpy version: 1.5.1 >>> | > >> | > > Libc version: >>> | > >> | > > >>> | > >> | > > Python packages (most are optional): >>> | > >> | > > >>> | > >> | > > Package Installed Version Path >>> | > >> | > > >>> | > >> | > minfx True Unknown >>> | > D:\Programs\relax\minfx >>> | > >> | > > bmrblib False >>> | > >> | > > numpy True 1.5.1 > C:\Program >>> | > >> | > > Files\Python26\lib\site-packages\numpy >>> | > >> | > > ScientificPython False >>> | > >> | > > wxPython True >>> | > >> | > > mpi4py False >>> | > >> | > > epydoc False >>> | > >> | > > optparse True 1.5.3 > C:\Program >>> | > >> | > > Files\Python26\lib\optparse.py >>> | > >> | > > Numeric False >>> | > >> | > > readline True > C:\Program >>> | > >> | > > Files\Python26\lib\site-packages\readline.py >>> | > >> | > > profile True > C:\Program >>> | > >> | > > Files\Python26\lib\profile.py >>> | > >> | > > bz2 True > C:\Program >>> | > >> | > > Files\Python26\DLLs\bz2.pyd >>> | > >> | > > gzip True > C:\Program >>> | > >> | > > Files\Python26\lib\gzip.py >>> | > >> | > > os.devnull True > C:\Program >>> | > >> | > > Files\Python26\lib\os.pyc >>> | > >> | > > >>> | > >> | > > Compiled relax C modules: >>> | > >> | > > Relaxation curve fitting: False >>> | > >> | > > --- >>> | > >> | > > >>> | > >> | > > It is clear that I don't have C library. At the moment, I > don't >>> | > need >>> | > >> | > it, but >>> | > >> | > > will try later with my data. >>> | > >> | > > >>> | > >> | > > Regards, >>> | > >> | > > Min-Kyu >>> | > >> | > > >>> | > >> | > > >>> | > >> | > > +------------------------------+ >>> | > >> | > > Cho, Min-Kyu >>> | > >> | > > Rm. 5110D MRBIII, 465 21st Ave S. >>> | > >> | > > Vanderbilt University School of Medicine, Nashville, TN > 37232- >>> | > 8725 >>> | > >> | > > Phone: 615-936-3757 / Fax: 615-936-2211 >>> | > >> | > > >>> | > >> | > > | > -----Original Message----- >>> | > >> | > > | > From: [email protected] >>> | > >> | > [mailto:[email protected]] On >>> | > >> | > > | > Behalf Of Edward d'Auvergne >>> | > >> | > > | > Sent: Tuesday, February 22, 2011 3:21 AM >>> | > >> | > > | > To: Cho, Min-Kyu >>> | > >> | > > | > Cc: [email protected] >>> | > >> | > > | > Subject: Re: ImporError >>> | > >> | > > | > >>> | > >> | > > | > Hi, >>> | > >> | > > | > >>> | > >> | > > | > Are you using the Win32 compiled version from >>> | > >> | > > | > http://www.nmr-relax.com/download.html? Could you run: >>> | > >> | > > | > >>> | > >> | > > | > $ relax --info >>> | > >> | > > | > >>> | > >> | > > | > and copy the result? The problem here is that the C >>> | > modules for >>> | > >> | > the >>> | > >> | > > | > relaxation curve-fitting of the R1 and R2 rates is either >>> | > not >>> | > >> | > compiled >>> | > >> | > > | > or the compiled version is incompatible with your >>> | > combination of >>> | > >> | > MS >>> | > >> | > > | > Windows version, Python version, and numpy version. > It may >>> | > be >>> | > >> | > that >>> | > >> | > > | > you are using a 64-bit version of Windows, in which case >>> | > the 32- >>> | > >> | > bit C >>> | > >> | > > | > module will not work. If you don't need to use this part >>> | > of relax, >>> | > >> | > > | > you can safely ignore this warning. >>> | > >> | > > | > >>> | > >> | > > | > However, if you do need it and you are brave, I have >>> | > created >>> | > >> | > > | > instructions on how to set up a development > environment on >>> | > Windows >>> | > >> | > to >>> | > >> | > > | > allow the C modules to be compiled: >>> | > >> | > > | > >>> | > >> | > > | > http://www.nmr-relax.com/windows_devel.html >>> | > >> | > > | > >>> | > >> | > > | > With scons and MS Visual C++ installed, it should be >>> | > possible to >>> | > >> | > > | > compile the module. >>> | > >> | > > | > >>> | > >> | > > | > Regards, >>> | > >> | > > | > >>> | > >> | > > | > Edward >>> | > >> | > > | > >>> | > >> | > > | > >>> | > >> | > > | > >>> | > >> | > > | > >>> | > >> | > > | > On 22 February 2011 06:13, Min-Kyu Cho <min- >>> | > >> | > [email protected]> >>> | > >> | > > | > wrote: >>> | > >> | > > | > > Hi Eddy, >>> | > >> | > > | > > >>> | > >> | > > | > > >>> | > >> | > > | > > >>> | > >> | > > | > > I got the following error when I executed 'relax' on >>> | > Window7; >>> | > >> | > > | > > >>> | > >> | > > | > > >>> | > >> | > > | > > >>> | > >> | > > | > > ImportError: relaxation curve fitting is > unavailable, the >>> | > >> | > > | > corresponding C >>> | > >> | > > | > > module have not been compiled. >>> | > >> | > > | > > >>> | > >> | > > | > > >>> | > >> | > > | > > >>> | > >> | > > | > > What should I do? >>> | > >> | > > | > > >>> | > >> | > > | > > >>> | > >> | > > | > > >>> | > >> | > > | > > Cheers, >>> | > >> | > > | > > >>> | > >> | > > | > > Min-Kyu >>> | > >> | > > | > > >>> | > >> | > > | > > >>> | > >> | > > | > > >>> | > >> | > > | > > _______________________________________________ >>> | > >> | > > | > > relax (http://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 >>> | > >> | > > | > > >>> | > >> | > > | > > >>> | > >> | > > >>> | > >> | > > >>> | > >> | > > _______________________________________________ >>> | > >> | > > relax (http://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 >>> | > >> | > > >>> | > >> >>> | > >> >>> | > > >>> >>> >>> _______________________________________________ >>> relax (http://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 >>> >> > > > > ------------------------------ > > _______________________________________________ > relax (http://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 > > End of relax-users Digest, Vol 56, Issue 4 > ****************************************** > > > Madeleine Strickland > > MCJC Group > N317, School of Chemistry, Bristol University > > > _______________________________________________ > relax (http://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 > _______________________________________________ relax (http://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
