Hi,
I've also cut and pasted the numbers into files, and run the script
using various versions of relax (1.2.10, 1.2.11, 1.2 repository line,
1.3.0), and all works fine for me too. I get Grace plots with all
points shown. I'm not sure what is happening, but we should be able
to get to the bottom of the problem. Johnny, were the data files
generated in MS Windows? Or on a Mac? Maybe it is the end of line
character being different on these platforms compared to Linux.
However python shouldn't have a problem with this. Which version of
Python are you using?
Regards,
Edward
On Tue, Mar 25, 2008 at 6:24 PM, Sébastien Morin
<[EMAIL PROTECTED]> wrote:
>
> Hi Johnny !
>
> I put all you data in the correct files on my laptop (names as in the
> script) and everything seems to work fine...
>
> I am using the 1.2 line, revision 5232 (subversion repository)...
>
> Please try to run the script with the attached files. Does it run well ?
> Are there differences with your own files ?
>
> Let me know if it works now...
>
> Cheers !
>
>
> Sébastien :)
>
>
>
>
>
>
>
> Johnny Croy wrote:
> Duh...my bad.
> On Mar 25, 2008, at 11:18 AM, Sébastien Morin wrote:
>
>
>
> Hi Johnny
>
> This is a private message (out of the mailing list).
>
> To get everything saved in the mailing list archive, please re-send
> this e-mail by replying all (me and the mailing list).
>
> Then, I'll send you my answer... :p
>
> Cheers,
>
>
> Séb :)
>
>
>
> Johnny Croy wrote:
>
>
> Seb,
>
> No problem...I didn't want to make an extremely long post on the
> first try. Here is the requested information.
>
> R1.dat file
>
> 31 Glu 1.145443882 0.057272194
> 32 Tyr 1.164796586 0.058239829
> 33 Lys 1.286855543 0.067178838
> 34 Ile 1.269676816 0.063483841
> 35 Gly 1.295773188 0.064788659
> 36 Glu 1.258616805 0.06293084
> 37 Leu 1.112491837 0.055624592
> 38 Thr 1.160197791 0.095182518
> 39 Phe 1.206707848 0.060335392
> 40 Gln 1.19092846 0.063554498
> 41 Ser 1.273809084 0.076303898
> 42 Ile 1.252180359 0.109824318
> 43 Arg 1.499938503 0.074996925
> 44 Ser 1.191667858 0.059583393
> 45 Ser 1.171024635 0.089300342
> 46 Gln 1.187752843 0.077913277
> 47 Glu 1.319825361 0.065991268
> 48 Leu 1.48565452 0.111707048
> 49 Gln 1.896734203 0.09483671
> 50 Lys 1.562314475 0.078115724
> 51 Lys 1.553675608 0.07768378
> 52 Asn 1.418429657 0.095146782
> 53 Thr 1.339907814 0.114773323
> 54 Ile 1.342170182 0.067108509
>
> R2.dat file
>
> 31 Glu 13.03407106 0.651703553
> 32 Tyr 16.98946653 1.170731842
> 33 Lys 16.64724488 1.374291449
> 34 Ile 14.56176372 0.981768177
> 35 Gly 16.76389727 0.838194864
> 36 Glu 14.49149349 0.724574675
> 37 Leu 16.68780455 0.834390228
> 38 Thr 18.43453895 3.355843235
> 39 Phe 17.07008979 1.342715745
> 40 Gln 19.703657 2.009887931
> 41 Ser 16.36687998 1.785653152
> 42 Ile 14.41836323 2.085960214
> 43 Arg 10.62812201 1.517689949
> 44 Ser 21.74574871 1.357631552
> 45 Ser 15.91039267 2.376737045
> 46 Gln 19.71336763 1.4472092
> 47 Glu 15.78357561 0.789178781
> 48 Leu 14.72016958 1.477130686
> 49 Gln 17.04884494 0.989417239
> 50 Lys 10.93123162 1.159309684
> 51 Lys 17.85809954 1.087170051
> 52 Asn 15.93447743 1.581082444
> 53 Thr 12.84868108 2.176528176
> 54 Ile 0.378840543 0.071234651
>
> NOE File
>
> 31 Glu 0.6462 0.0867
> 32 Tyr 0.6927 0.1418
> 33 Lys 0.6937 0.05
> 34 Ile 0.6797 0.05
> 35 Gly 0.6467 0.1091
> 36 Glu 0.6007 0.0549
> 37 Leu 0.6835 0.05
> 38 Thr 0.8187 0.05
> 39 Phe 0.7406 0.05
> 40 Gln 0.76 0.05
> 41 Ser 0.8434 0.0926
> 42 Ile 0.7271 0.0676
> 43 Arg 0.4559 0.3041
> 44 Ser 0.745 0.0541
> 45 Ser 0.6798 0.0617
> 46 Gln 0.7618 0.05
> 47 Glu 0.7454 0.0914
> 48 Leu 0.6044 0.05
> 49 Gln 0.5899 0.0861
> 50 Lys 0.5631 0.0997
> 51 Lys 0.4634 0.1099
> 52 Asn 0.6635 0.05
> 53 Thr 0.574 0.05
> 54 Ile 0.3808 0.1667
>
> Seq File
>
> 31 Glu
> 32 Tyr
> 33 Lys
> 34 Ile
> 35 Gly
> 36 Glu
> 37 Leu
> 38 Thr
> 39 Phe
> 40 Gln
> 41 Ser
> 42 Ile
> 43 Arg
> 44 Ser
> 45 Ser
> 46 Gln
> 47 Glu
> 48 Leu
> 49 Gln
> 50 Lys
> 51 Lys
> 52 Asn
> 53 Thr
> 54 Ile
>
> jw_mapping Script
>
> # Script for reduced spectral density mapping.
>
> # Create the run.
> name = 'jw'
> run.create(name, 'jw')
>
> # Nuclei type
> nuclei('N')
>
> # Load the sequence.
> sequence.read(name, 'Pot1pN_free_seq.txt')
>
> # Load the relaxation data.
> relax_data.read(name, 'R1', '500', 500.0 * 1e6,
> 'R1_f_500_5percent.txt')
> relax_data.read(name, 'R2', '500', 500.0 * 1e6,
> 'R2_f_500_5percent.txt')
> relax_data.read(name, 'NOE', '500', 500.0 * 1e6,
> 'NOE_f_5percent.txt')
>
> # Set the bond length and CSA values.
> value.set(name, 1.02 * 1e-10, 'bond_length')
> value.set(name, -172 * 1e-6, 'csa')
>
> # Select the frequency.
> jw_mapping.set_frq(name, frq=500.0 * 1e6)
>
> # Reduced spectral density mapping.
> calc(name)
>
> # Monte Carlo simulations.
> monte_carlo.setup(name, number=500)
> monte_carlo.create_data(name)
> calc(name)
> monte_carlo.error_analysis(name)
>
> # Create grace files.
> grace.write(name, y_data_type='j0', file='j0.agr', force=1)
> grace.write(name, y_data_type='jwx', file='jwx.agr', force=1)
> grace.write(name, y_data_type='jwh', file='jwh.agr', force=1)
>
> # View the grace files.
> grace.view(file='j0.agr')
> grace.view(file='jwx.agr')
> grace.view(file='jwh.agr')
>
> # Finish.
> results.write(run=name, file='results', force=1)
> state.save('save', force=1)
>
> Version of relax is 1.2.11 on Red Hat Linux Enterprise 5.
>
> Please let me know if you need anything further.
>
> Best regards,
>
> J
>
>
> On Mar 25, 2008, at 10:40 AM, Sébastien Morin wrote:
>
>
>
> Hi Johnny !
>
> I would be helpful if you could post, let's say, the first 10
> lines of each input file as well as the complete script you used.
>
> Moreover, it could be also useful to know which version of relax
> you use...
>
> Cheers !
>
>
> Séb :)
>
>
>
> Johnny Croy wrote:
>
>
> Hello,
>
> I am new to using relax, but I have been running into a problem
> with reading data into relax using the jw_mapping.py sample
> script. I have three separate files for noe, r1 and r2 all
> collected at 500 MHZ. These are tab delimitated files that
> contain residue #, residue name, value and error in columns 0-3,
> respectively. Also a file containing the sequence, residue #
> and name in cols 0 and 1, respectively was generated. These
> files were substituted into the script in the appropriate places
> and frequencies were changed. When the script is invoked using
> 'relax jw_mapping.py' it runs through to the end displaying the
> grace plots and the appropriate output files are created.
> However, only the first residue in the file is analyzed. How do
> I tell relax to read in the whole list?
>
> Thanks in advance for your help!
>
> Best regards,
>
> Johnny Croy
> CU Boulder
>
> _______________________________________________
> 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
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>
>
>
>
>
> _______________________________________________
> 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
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>
>
>
> NOE File
>
> 31 Glu 0.6462 0.0867
> 32 Tyr 0.6927 0.1418
> 33 Lys 0.6937 0.05
> 34 Ile 0.6797 0.05
> 35 Gly 0.6467 0.1091
> 36 Glu 0.6007 0.0549
> 37 Leu 0.6835 0.05
> 38 Thr 0.8187 0.05
> 39 Phe 0.7406 0.05
> 40 Gln 0.76 0.05
> 41 Ser 0.8434 0.0926
> 42 Ile 0.7271 0.0676
> 43 Arg 0.4559 0.3041
> 44 Ser 0.745 0.0541
> 45 Ser 0.6798 0.0617
> 46 Gln 0.7618 0.05
> 47 Glu 0.7454 0.0914
> 48 Leu 0.6044 0.05
> 49 Gln 0.5899 0.0861
> 50 Lys 0.5631 0.0997
> 51 Lys 0.4634 0.1099
> 52 Asn 0.6635 0.05
> 53 Thr 0.574 0.05
> 54 Ile 0.3808 0.1667
>
> Seq File
>
> 31 Glu
> 32 Tyr
> 33 Lys
> 34 Ile
> 35 Gly
> 36 Glu
> 37 Leu
> 38 Thr
> 39 Phe
> 40 Gln
> 41 Ser
> 42 Ile
> 43 Arg
> 44 Ser
> 45 Ser
> 46 Gln
> 47 Glu
> 48 Leu
> 49 Gln
> 50 Lys
> 51 Lys
> 52 Asn
> 53 Thr
> 54 Ile
>
> R1.dat file
>
> 31 Glu 1.145443882 0.057272194
> 32 Tyr 1.164796586 0.058239829
> 33 Lys 1.286855543 0.067178838
> 34 Ile 1.269676816 0.063483841
> 35 Gly 1.295773188 0.064788659
> 36 Glu 1.258616805 0.06293084
> 37 Leu 1.112491837 0.055624592
> 38 Thr 1.160197791 0.095182518
> 39 Phe 1.206707848 0.060335392
> 40 Gln 1.19092846 0.063554498
> 41 Ser 1.273809084 0.076303898
> 42 Ile 1.252180359 0.109824318
> 43 Arg 1.499938503 0.074996925
> 44 Ser 1.191667858 0.059583393
> 45 Ser 1.171024635 0.089300342
> 46 Gln 1.187752843 0.077913277
> 47 Glu 1.319825361 0.065991268
> 48 Leu 1.48565452 0.111707048
> 49 Gln 1.896734203 0.09483671
> 50 Lys 1.562314475 0.078115724
> 51 Lys 1.553675608 0.07768378
> 52 Asn 1.418429657 0.095146782
> 53 Thr 1.339907814 0.114773323
> 54 Ile 1.342170182 0.067108509
>
> R2.dat file
>
> 31 Glu 13.03407106 0.651703553
> 32 Tyr 16.98946653 1.170731842
> 33 Lys 16.64724488 1.374291449
> 34 Ile 14.56176372 0.981768177
> 35 Gly 16.76389727 0.838194864
> 36 Glu 14.49149349 0.724574675
> 37 Leu 16.68780455 0.834390228
> 38 Thr 18.43453895 3.355843235
> 39 Phe 17.07008979 1.342715745
> 40 Gln 19.703657 2.009887931
> 41 Ser 16.36687998 1.785653152
> 42 Ile 14.41836323 2.085960214
> 43 Arg 10.62812201 1.517689949
> 44 Ser 21.74574871 1.357631552
> 45 Ser 15.91039267 2.376737045
> 46 Gln 19.71336763 1.4472092
> 47 Glu 15.78357561 0.789178781
> 48 Leu 14.72016958 1.477130686
> 49 Gln 17.04884494 0.989417239
> 50 Lys 10.93123162 1.159309684
> 51 Lys 17.85809954 1.087170051
> 52 Asn 15.93447743 1.581082444
> 53 Thr 12.84868108 2.176528176
> 54 Ile 0.378840543 0.071234651
>
> _______________________________________________
> 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
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>
>
_______________________________________________
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