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
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>>>>
>>>>
>>>
>>
>>
>
_______________________________________________
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