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
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_______________________________________________
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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
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Re: Spectral Density Mapping Problem