Hi all ! I ran the script with relax 1.2.11 and it works also fine for me. Did you run the test-suite (relax --test-suite) ? Are there any errors ? I would also point the end of lines or the character encoding... On your Red Hat system, what happens if you type : file Pot1pN_free_seq.txt R1_f_500_5percent.txt R2_f_500_5percent.txt NOE_f_5percent.txt Is the output as follows : Pot1pN_free_seq.txt: ASCII text R1_f_500_5percent.txt: ASCII text R2_f_500_5percent.txt: ASCII text NOE_f_5percent.txt: ASCII text Good luck ! Séb Edward d'Auvergne wrote: 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 <sebastien.morin.1@xxxxxxxxx> 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 relax-users@xxxxxxx 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 relax-users@xxxxxxx 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 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 relax-users@xxxxxxx 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 |