Converting Peak Lists into AutoAssign Format
Registering AutoAssign Peak Lists
Manipulating Peak Lists
Evaluating the Quality of Peak Lists
Evaluating Assignment Results
Manipulating BMRB (NMRStar) Files
The first step in using AutoAssign and many other parts of AutoPeak is converting peaks lists into AutoAssign format.Programs:
extract_columns.pl - extracts columns from text files.
create_peak_list.pl - creates a peak list given peak information in separate columns.
sparkyPks2pks.pl - create a peak list given the shift values and intensity in separate columns. It also tries to assert a HN, N15, HX, CX, CO and X dimension ordering.
1) Convert an HNCACB -type peak list into AutoAssign format.
The raw HNCACB-type peak file in the following format:
2 126.257 46.356 7.965 2 U 3.396e+04 4.86e+02 a 0 30103 30105 30104 0The following series of commands will create a peak list in the AutoAssign format:
4 124.691 61.261 9.144 2 U 4.550e+02 3.54e+02 a 0 30203 30205 30204 0
5 124.050 54.715 7.640 2 U 6.764e+03 5.84e+02 a 0 30303 30305 30304 0
6 123.694 53.532 8.140 2 U 2.642e+04 4.75e+02 a 0 30403 30405 30404 0
7 123.694 59.841 7.878 2 U 7.815e+03 5.44e+02 a 0 30503 30505 30504 0
...% extract_columns.pl 4 2 3 7 < raw_peak_list.txt > extracted_peak_list.txtThe resulting HNCACB-type peak file will look like this:
% create_peak_list.pl extracted_peak_list.txt HNCACB hncacb.pks#Index 1Dim 2Dim 3Dim Intensity Workbook
1 7.965 126.257 46.356 3.396e+04 HNCACB
2 9.144 124.691 61.261 4.550e+02 HNCACB
3 7.640 124.050 54.715 6.764e+03 HNCACB
4 8.140 123.694 53.532 2.642e+04 HNCACB
5 7.878 123.694 59.841 7.815e+03 HNCACB
...
For good performance from AutoAssign and other AutoPeak programs that compare peak lists, peak lists must be registered to each other in their alignable dimensions. Even though spectra may be aligned by hand in spectra visualization software, differences in data collection and processing as well as imperfections in phasing, peak picking, and peak centering can create deviations that reduce performance. Also, registration of peaks lists gives valuable statistical information on how comparable peaks lists are. This is useful in evaluation peak list quality and determining match tolerances.
Normally, a star registration strategy gives good registration results. A typical application of a star strategy is registering all the peaks lists to the HSQC in the matching amide 1H and 15N dimensions followed by registering all alphiphatic carbon containing peak lists to the HNCACB-type peak list. If HNHA/HNcoHA or HNCO/HNcaCO combinations of peak lists are present, then these pairwise registrations are performed as well.
calculate_registration - calculates the registration (shifting) of one peak list against another.
apply_shifting.pl - adjusts peaks chemical shifts using the given shifting.
calculate_registration:Examples:
Check the dimensions in the peak lists if calculate_registration does not find an initial registration.
1) Register an HNcoCA peak list to an HSQC peak list.
Calculating the registration is done with the following command:
% calculate_registration hncoca.pks hsqc.pksThis generates the following output:
Final ResultsThe following command applies the shifting to create an aligned HNcoCA peak list:
Raw Robustness: 92.734 out of 95
Robustness: 64.6922 out of 95
Input Dimensions: 1 2 3
Full Registration: -0.0109206 0.132316 ------
Weighted Registration: -0.0107468 0.132745 ------
Full STD: 0.000922378 0.00725433 ------
Weighted STD: 0.000678018 0.00525216 ------
Full Skewness: -0.958115 -0.867331 ------
Weighted Skewness: 0.00108908 0.0305068 ------
Full Kurtosis: 4.70341 2.72701 ------
Weighted Kurtosis: 0.157536 0.0175747 ------
% apply_shifting.pl hncoca.pks HNcoCA hncoca2.pks -0.0107 0.1327
Many times peak lists must be manipulated in various ways to create a usable AutoAssign dataset. These manipulations are normally required to handle alternate data collection strategies using fewer experiments. But some of the manipulations are useful in implementing robust automatic restrictive peak picking strategies or in handling datasets with signficant numbers of residues in multiple conformations.
Using the AutoPeak programs to perform these manipulations has the added benefit of keeping a log of the manipulations in the "File History" of each peak list. This feature is invaluable for keeping up with where peak lists came from and how they have been manipulated.
average_duplicates.pl - create a set of average peaks from groups of duplicate peaks.
change_phase.pl - changes the sign of the peak intensities.
concatenate.pl - concatenates multiple peak files.
convert_rd_experiment - extracts the projected dimension in a reduced dimensionality experiment.
extract_dims.pl - extracts and rearranges peak dimensions of a peak file.
extract_duplicates.pl - extracts duplicate or nonduplicate peaks.
extract_by_dup_count.pl - extract peak duplicates with a certain peak count.
extract_by_filter.pl - extracts peaks that match (or don't match) a filter list.
extract_by_intensity.pl - extract a certain fraction of strong peaks.
extract_by_intensity2.pl - extract peaks above a fraction of the average/top peak.
extract_by_intensity3.pl - extract peaks above a threshhold.
extract_by_phase.pl - extract positive or negative intensity peaks.
extract_by_shift.pl - extract peaks with chemical shifts above or below certain values.
extract_by_shift_range.pl - extract peaks with chemical shifts within a range of values.
file_history.pl - print File History of a peak file.
match_recombine.pl - create new peaks from parts of other peaks.
pks2SparkyPks.pl - converts an AutoAssign peak list file to a Sparky peak list file.
pks2Xeasy.pl - convert an AutoAssign peak list into Xeasy format.
remove_peaks.pl - removes peaks from a peak list with the given indeces.
tag_peaks.pl - extract a group of peaks using a set of filter peaks and tag them.
1) Generate an HSQC peak list from an HNCO peak list.
Given the "hnco.pks" HNCO peak list that looks like:
#Index 1Dim 2Dim 3Dim Intensity WorkbookThe following command will extract the first two dimensions to create an HSQC peak list:
1 8.479 123.157 180.112 1.0612e+06 HNCO
2 8.811 123.028 179.764 8.7698e+05 HNCO
3 8.349 120.988 179.768 1.0079e+06 HNCO
4 7.566 120.516 179.758 1.5093e+06 HNCO
5 7.615 117.932 179.215 1.1491e+06 HNCO
...
% extract_dims.pl hnco.pks HSQC hsqc.pks 1 2This creates the "hsqc.pks" HSQC peak list that looks like:
#Index 1Dim 2Dim Intensity Workbook
1 8.479 123.157 1.0612e+06 HSQC
2 8.811 123.028 8.7698e+05 HSQC
3 8.349 120.988 1.0079e+06 HSQC
4 7.566 120.516 1.5093e+06 HSQC
5 7.615 117.932 1.1491e+06 HSQC
...
2) Generate an HNCA-type peak list from a CA/CB phase labelled HNCACB-type peak list.
Given the "hncacb.pks" HNCACB-type peak list that looks like:
#Index 1Dim 2Dim 3Dim Intensity WorkbookThe negative intensity peaks are the CA peaks.
1 7.721 116.744 21.733 1.2652e+06 HNCACB
2 8.374 117.233 33.196 3.488e+05 HNCACB
3 8.301 117.234 32.545 8.8283e+05 HNCACB
4 8.374 117.217 68.946 7.9682e+05 HNCACB
5 8.376 117.24 63.796 -7.6645e+05 HNCACB
6 8.377 117.244 61.818 -4.0926e+05 HNCACB
7 8.302 117.224 54.735 -1.4108e+06 HNCACB
8 8.304 117.237 46.501 -4.6939e+05 HNCACB
...
The following command extract the peaks with the negative intensities from an HNCACB-type peak list:
% extract_by_phase.pl hncacb.pks negative HNCA hnca.pksThis creates an HNCA-type peak list that looks like:
#Index 1Dim 2Dim 3Dim Intensity Workbook
1 8.376 117.24 63.796 -7.6645e+05 HNCA
2 8.377 117.244 61.818 -4.0926e+05 HNCA
3 8.302 117.224 54.735 -1.4108e+06 HNCA
4 8.304 117.237 46.501 -4.6939e+05 HNCA
...
3) Generate an HNcoCA-type peak list using an HNcoCACB-type and HNCA-type peak lists.
Given the "hnca.pks" HNCA-type peak list looks like:4) Generate an average HSQC from a composite of the other peak lists.
#Index 1Dim 2Dim 3Dim Intensity Workbook
1 8.376 117.24 63.796 -7.6645e+05 HNCA
2 8.377 117.244 61.818 -4.0926e+05 HNCA
3 8.302 117.224 54.735 -1.4108e+06 HNCA
4 8.304 117.237 46.501 -4.6939e+05 HNCA
...
Given the "hncocacb.pks" HNcoCACB-type peak list looks like:
#Index 1Dim 2Dim 3Dim Intensity WorkbookThe following command extracts the peaks from "hnca.pks" that matches peaks in "hncocacb.pks":
1 8.379 117.216 61.816 1.6974e+06 HNcoCACB
2 8.379 117.216 33.294 9.6913e+05 HNcoCACB
3 8.3 117.211 46.479 1.3929e+06 HNcoCACB
4 8.616 117.15 66.864 1.0037e+06 HNcoCACB
...
% extract_by_filter.pl hnca.pks hncocacb.pks inclusive HNcoCA hncoca.pks 0.02 0.3 0.4This creates an HNcoCA-type peak list that looks like:
#Index 1Dim 2Dim 3Dim Intensity Workbook
1 8.377 117.244 61.818 -4.0926e+05 HNcoCA
2 8.304 117.237 46.501 -4.6939e+05 HNcoCA
...
Given a dataset that has twice the number of HSQC peaks that are expected given the sequence.
This is a strong indication of multiple conformations.
AutoAssign is having problems working through the large number of spin systems.
The follow pair of commands concatenates a group of peak lists and creates a composite HSQC peak list from the most complete spin systems:
% concatenate.pl pre_hsqc.pks HSQC hsqc.pks hnco.pks hncacb.pks hncocacb.pks hncoca.pks hnca.pks hnha.pks
% average_duplicates.pl pre_hsqc.pks HSQC hsqc_average.pks -min 8 0.03 0.1
5) Generate HNCA-type and HNHA-type peak lists from a reduced dimensionality HNCAHA peak list.
Given the "hncaha_rd.pks" RD HNCAHA peak list looks like:
#Index 1Dim 2Dim 3Dim Intensity WorkbookThe following command converts the peak triplets in "hncaha_rd.pks" into 4D peak equivalents:
1 7.637 129.737 59.037 -3.126e+04 HNCAHA
2 7.692 129.737 59.119 -4.023e+03 HNCAHA
3 8.038 128.735 57.535 -7.771e+04 HNCAHA
4 8.411 128.400 52.359 -1.760e+04 HNCAHA
5 7.210 126.061 53.675 -6.397e+04 HNCAHA
...
250 7.889 124.055 39.492 6.637e+04 HNCAHA
251 7.887 124.055 38.172 3.709e+04 HNCAHA
252 8.138 119.376 46.162 4.076e+04 HNCAHA
253 8.139 119.376 39.325 2.837e+04 HNCAHA
254 8.168 118.373 46.747 5.668e+04 HNCAHA
255 8.168 118.373 46.090 1.652e+04 HNCAHA
256 8.536 120.713 44.570 6.805e+04 HNCAHA
...
% convert_rd_experiment hncaha_rd.pks hncaha_4D.pks 3 0.0 3.97603 -range 2.9 5.5 -template average -print expanded -sign neg -use_two -match_int 0.9 -weight 0.5 -tol 0.03 0.3 0.3This creates a 4D HNCAHA peak list that looks like:
#Index 1Dim 2Dim 3Dim 4Dim Intensity WorkbookThe following commands extracts the HNCA-type and HNHA-type peak lists from the 4D HNCAHA peak list:
1 7.64 129.737 59.067 4.449 16026.666 HNCAHA
2 7.642 129.737 61.367 4.111 7280 HNCAHA
3 7.69 129.737 59.092 4.461 8919 HNCAHA
4 8.039 128.735 57.529 4.175 30890 HNCAHA
5 8.039 128.735 63.614 4.46 10153.333 HNCAHA
6 8.411 128.4 52.357 4.288 11016.666 HNCAHA
7 8.41 128.4 56.478 4.316 557.666 HNCAHA
8 7.212 126.061 53.614 4.477 18183.333 HNCAHA
9 7.212 126.061 55.829 4.5 1988.666 HNCAHA
...
% extract_dims.pl hncaha_4D.pks HNCA hnca.pks 1 2 3
% extract_dims.pl hncaha_4D.pks HNHA hnha.pks 1 2 4
The first step in obtaining correct assignments from AutoAssign is to give AutoAssign a good dataset. Towards this goal, one must evaluate the quality of the peak lists in the dataset. Evaluations are done on each peak list and on the set of peak lists.
calculate_registration - calculates the registration (shifting) of one peak list against another.
examine_spin_systems.pl - groups peaks into spin systems and examines them for completeness and overlap.
1) Uses calculate_registration to detect a poorly unalignable peak list.
The following command checks how alignable an HNCO peak list is to an HNcaCO peak list:
% calculate_registration hnco.pks hncaco.pksThis generates the following output:
Final ResultsThe high STD for the third dimension (carbonyl) and few matching peaks shows a clear problem in aligning these two peak lists. One or both peak lists may be flawed.
Raw Robustness: 56 out of 156
Robustness: 49.6801 out of 156
Input Dimensions: 1 2 3
Full Registration: 0.0008543 0.0715716 0.51375
Weighted Registration: 0.0005342 0.0730397 0.613312
Full STD: 0.00545457 0.0354198 2.07691
Weighted STD: 0.00370256 0.0327938 1.85157
Full Skewness: -4.74346e-05 -0.264039 -0.240244
Weighted Skewness: -0.0712982 -0.280238 -0.17169
Full Kurtosis: 2.60191 -0.446117 0.391656
Weighted Kurtosis: 1.31327 -0.219108 0.270923
2) Examines all the peak lists by how well they organize into spin systems.
The following command concatenates all the peak lists together:
% concatenate.pl all_peaks.pks - -old_index hnca.pks hncacb.pks hnco.pks hncoca.pks hncocacb.pks hsqc.pksThe following command groups the peaks into spin systems and examines each spin system:
% examine_spin_systems.pl all_peaks.pks report.pks 0.03 0.35 0.4 0.05 0.35This generates the following output:
#Index 1Dim 2Dim 3Dim Intensity WorkbookThis report can direct peak picking for missing peaks in the different peak lists. For example "Spin System 2" is missing 3 to 4 different peaks from different peak lists.
#
#
#
#
# Spin System 0
#
# Gly Intra Flags: 2
#
1 7.910 108.152 45.685 361023 HNCA
264 7.914 108.271 55.066 146662 HNCA
23 7.90550002 108.1782337 45.629 1368605 HNCACB
323 7.91150002 108.1022337 29.105 -214385 HNCACB
324 7.91050002 108.1442337 55.189 182674 HNCACB
42 7.90656298 108.15922925 176.378201 5550650 HNCO
8 7.907239426 108.1589011 55.1338 434843 HNcoCA
188 7.90574684 108.1821777 55.154111 916206 HNcoCACB
309 7.90574684 108.1401777 29.094111 -710884 HNcoCACB
41 7.906 108.150 610197 HSQC
#
#
#
#
# Spin System 1
#
# Incomplete Flags: 1
# HNCA -1
# Gly Intra Flags: 2
#
2 8.280 108.567 45.279 997229 HNCA
250 8.27450002 108.5862337 54.951 406760 HNCACB
325 8.27750002 108.5862337 32.005 -377034 HNCACB
327 8.27650002 108.5942337 45.248 4258708 HNCACB
47 8.27656298 108.54622925 174.120201 12943344 HNCO
9 8.277239426 108.5529011 55.0598 1189475 HNcoCA
231 8.27574684 108.5511777 32.289111 -1634500 HNcoCACB
311 8.27274684 108.5341777 55.125111 2088785 HNcoCACB
45 8.282 108.564 1333516 HSQC
#
#
#
#
# Spin System 2
#
# Incomplete Flags: 4
# HNcoCA -1 HNCA -1 HNcoCACB -1 HNCACB -1
#
3 8.332 108.676 45.093 6166932 HNCA
24 8.32950002 108.6892337 31.717 -1065387 HNCACB
326 8.32850002 108.6952337 45.076 30771032 HNCACB
46 8.32856298 108.67522925 174.931201 108363768 HNCO
325 8.32874684 108.6701777 45.216111 42570612 HNcoCACB
44 8.329 108.667 5176627 HSQC
#
...
The assignment results from AutoAssign must be evaluated. The typical problems arise at the ends of assigned segments and with overlapped spin systems. Also checking assignments that do not have CB assignments coming from both intra and sequential peaks should be checked as well.
To aid in the evaluation are programs for comparison of BMRB assignments to expected values for each type of resonance. There are also evaluation with respect to other types of data including hCCcoNH TOCSY and 15N-Edited NOESY. There are also other evaluations that determines if the assigned segments of spin systems break inherent typing degeneracy seen in the sequence.
bmrb2cmap.pl - converts bmrb format to cmap format.
compare_bmrb.pl - compares two bmrb files and returns how well they match.
compare_cmap.pl - compares two CMap files and returns how well they match.
bmrb_assign_spl.pl - assigns the spectral_peak_lists in a BMRB file.
dyanaUPL2cmap.pl - converts the backbone NOEs from a DYANA UPL constraint file to the CMap format.
jval2bmrb.pl - converts AutoStructure Input J HNHA values into BMRB coupling constants save frame.
missing_shifts.pl - reports the missing AtomTypes in a given BMRB file.
pks2bmrb.pl - Converts AutoAssign peak list into BMRB spectral peak list save frame.
sec2bmrb.pl - converts AutoStructure output .sec file into BMRB secondary_structure save frame.
typing_degeneracy.pl - calculates the typing degeneracy for a given sequence.
validate_assignments.pl - validates assignments in bmrb format.
1) Checks a BMRB file for missing assignments.
The following command scans a BMRB file for missing assignments:
% missing_shifts.pl -expected -printstats assignments.bmrbThis produces the following report of what is missing:
M1: CE 17.43 CG 32.13 H 8.29 HA 4.41 HB2 2.01 HB3 2.01 HE 1.84 HG2 2.47 HG3 2.46 N 120.22The missing assignments are organized by residue with their expected values. This is is useful in directly looking for these assignments. There is also a summary report for each resonance class.
G2: HA3 3.98
H3: C 174.97 CD2 119.64 CE1 136.09 CG 130.59 HB2 3.1 HB3 3.13 HD1 11.56 HD2 7.1 HE1 8.11 HE2 10.99 ND1 192.74 NE2 180.95
H4: C 174.97 CD2 119.64 CE1 136.09 CG 130.59 HA 4.62 HB2 3.1 HB3 3.13 HD1 11.56 HD2 7.1 HE1 8.11 HE2 10.99 ND1 192.74 NE2 180.95
H8: CA 55.99 CB 29.67 CD2 119.64 CE1 136.09 CG 130.59 H 8.26 HA 4.62 HB2 3.1 HB3 3.13 HD1 11.56 HD2 7.1 HE1 8.11 HE2 10.99 N 118.7 ND1 192.74 NE2 180.95
S9: CB 63.77 HB2 3.84 HB3 3.85 HG 5.19
H10: CD2 119.64 CE1 136.09 CG 130.59 HB2 3.1 HB3 3.13 HD1 11.56 HD2 7.1 HE1 8.11 HE2 10.99 ND1 192.74 NE2 180.95
M11: CE 17.43 CG 32.13 HB2 2.01 HB3 2.01 HE 1.84 HG2 2.47 HG3 2.46
A12: HB 1.38
A13: HB 1.38
...
Percentage of AtomTypes >>
C :: 150 / 187 = 80.214%
CA :: 185 / 187 = 98.930%
CB :: 164 / 168 = 97.619%
CD :: 0 / 47 = 0.000%
CD1 :: 0 / 27 = 0.000%
CD2 :: 0 / 30 = 0.000%
CE :: 0 / 31 = 0.000%
...
2) Statistically validate each assignment in a BMRB file.
The following command checks each assignment in the BMRB file:
% validate_assignments.pl assignments.bmrbThis produces the following report:
M1 Overall: Consistent Typing: Indeterminable SRO: Consistent C Shifts: Indeterminable H Shifts: IndeterminableThe report is broken down by residue with a summary of suspicious and erroneous chemical shifts at the end. This program checks each chemical shift against its expected values and types each residue using the aliphatic carbon chemical shifts. It also reports unknown resonance types and duplicate entries.
A2 Overall: Consistent Typing: Consistent SRO: Consistent C Shifts: Consistent H Shifts: Consistent
PRTL>> A 0.8541 M 0.1374 L 0.0064 V 0.0009 I 0.0007 T 0.0001
C Shift Assignments>> C :: 179.3 CA :: 51.5 CB :: 19.4
H Shift Assignments>> H :: 8.57 HA :: 4.04 HB :: 1.46
K3 Overall: Misassigned Typing: Suspicious SRO: Consistent C Shifts: Misassigned H Shifts: Consistent
PRTL>> M 0.7431 Q 0.184 E 0.0552 Y 0.0099 R 0.0055 F 0.0011 I 0.0009
C Shift Assignments>> C :: 176.4 CA :: 56.6 CB :: 32.7 CG :: 32.7(M)
Ave C Shift Values>> C :: 176.46 CA :: 56.84 CB :: 32.83 CG :: 24.91 CD :: 28.78 CE :: 41.78
H Shift Assignments>> H :: 8.58 HA :: 4.14 HB2 :: 1.82 HB3 :: 1.82 HG2 :: 1.51 HG3 :: 1.51
...
Error Summary:
K3 Typing: Suspicious
K3 CG = 32.7(M), Expected = 24.91, Std = 1.3100, ChiSquare = 2.7383e-09
P8 HD2 = 0.82(M), Expected = 3.64, Std = 0.3600, ChiSquare = 4.7510e-15
P8 HD3 = 0.82(M), Expected = 3.63, Std = 0.4000, ChiSquare = 2.1407e-12
Q9 Typing: Mistyped
Q9 CD = 29.1(M), Expected = 179.68, Std = 1.1700, ChiSquare = 0.0000e+00
Q9 HG2 = 3.31(S), Expected = 2.32, Std = 0.2900, ChiSquare = 6.4065e-04
Q9 HG3 = 3.31(S), Expected = 2.32, Std = 0.2900, ChiSquare = 6.4065e-04
...
3) Adds additional types of data to a BMRB file and then converts it to a CMap file for visualization of assignment results.
The following commands converts AutoAssign peak lists into spectral peak list save frames and appends them to a BMRB file:
% pks2bmrb.pl hsqc.pks assignments_plus.bmrb -appendThe following command assigns the unassigned spectral peak list save frames:
% pks2bmrb.pl hnco.pks assignments_plus.bmrb -append
% pks2bmrb.pl hnca.pks assignments_plus.bmrb -append
% pks2bmrb.pl hncoca.pks assignments_plus.bmrb -append
% pks2bmrb.pl hncacb.pks assignments_plus.bmrb -append
% pks2bmrb.pl hncocacb.pks assignments_plus.bmrb -append
% pks2bmrb.pl hnha.pks assignments_plus.bmrb -append
% pks2bmrb.pl hncoha.pks assignments_plus.bmrb -append
% pks2bmrb.pl c_hccconh.pks assignments_plus.bmrb -append
% pks2bmrb.pl h_hccconh.pks assignments_plus.bmrb -append
% create_assigned_peaklist.pl assignments_plus.bmrb assignments_plus2.bmrbThe following command converts AutoStructure HNHA J coupling values and appends them to the BMRB file:
% jval2bmrb.pl hnha_j.txt assignments_plus2.bmrb -appendThe following command converts the BMRB file to CMap file format:
% bmrb2cmap.pl assignments_plus2.bmrb assignments_plus2.cmapThe following command converts dyana UPL backbone NOE constraints and appends them to the CMap file:
% dyanaUPL2cmap.pl -append n15_noesy.upl assignments_plus2.cmapThe following is the visualization of the CMap file using the AutoAssign CMap Image Editor:
![]()
This visualization contains all the Resonance Rows as well as NOE Connectivity Rows, a J Coupling Row, and a Secondary Structure Row.
4) Analyzes the linkage strength and typing degeneracy of assigned spin system segments in a CMap file.
The following command analyzes the typing degeneracy of the assigned segments:
% typing_degeneracy.pl -input assignments.cmap -output report.cmapThis produces the following output:
Suspicious Spin System Segments:This shows three segments that are not as uniquely typed as one would hope. This does not mean they are misassigned; however, they do deserve a closer look.
Segment - Suspicion
-------------------
10_PAL - segment mapping is not unique - Likelyhood = 4.8444e-01
Likelyhood(19_GAF) = 1.4526e-01 Ratio = 3.3351
Likelyhood(78_SAN) = 5.4626e-01 Ratio = 0.8868
Likelyhood(100_ECF) = 3.4376e-03 Ratio = 140.9238
Likelyhood(125_VAL) = 4.8444e-01 Ratio = 1.0000
Likelyhood(144_KAI) = 3.3615e-03 Ratio = 144.1141
24_GHFKD - segment mapping is not unique - Likelyhood = 7.9198e-01
Likelyhood(30_KRLYC) = 3.2701e-02 Ratio = 24.2192
Likelyhood(53_REKSD) = 2.0389e-03 Ratio = 388.4319
Likelyhood(58_PHIKL) = 8.3012e-02 Ratio = 9.5406
Likelyhood(60_IKLQL) = 7.5661e-03 Ratio = 104.6748
Likelyhood(84_AMKED) = 1.0668e-03 Ratio = 742.3855
Likelyhood(99_DECFF) = 7.4711e-02 Ratio = 10.6005
Likelyhood(100_ECFFF) = 6.8821e-02 Ratio = 11.5079
Likelyhood(131_GQYKL) = 2.9742e-01 Ratio = 2.6628
87_EDGR - segment mapping is not unique - Likelyhood = 4.4020e-01
Likelyhood(45_PDGR) = 8.8520e-04 Ratio = 497.2905
Likelyhood(49_VDGV) = 7.2126e-03 Ratio = 61.0327
...
The following is the visualization of the CMap file generated by typing_degeneracy.pl:
![]()
The Degeneracy Length Row shows the minimum degeneracy of overlapping sequence segments. The parts in red shows spin system segments not long enough to break this degeneracy. The Linkage Strength Row shows the number of resonance rungs (and/or NOE connectivity rungs) indicating that the neighboring spin systems are linked.
NMR Star is the file format for depositing NMR assignments with the BioMagneticResBank. AutoAssign produces assignments in NMR Star (BMRB) format. However, a complete BMRB entry contains more than the assigned chemical shift save frame. AutoPeak contains a collection of BMRB conversion and manipulation programs for comparing assignments, validating assignments, and creating a (more) complete BMRB entry.Programs:
There are also many conversion programs from BMRB to other formats for use inside AutoAssign and Sparky.
bmrb2cmap.pl - converts bmrb format to cmap format.Examples:
bmrbACS2pks.pl - converts BMRB assigned chemical shifts frame to an AutoAssign peak list.
bmrbACS2SparkyPks.pl - converts bmrb assigned chemical shift save frame to Assigned Sparky Peak List format.
bmrb2AutoStructure.pl - converts bmrb format to AutoStructure Resonance List format.
bmrbSPL2pks.pl - converts BMRB spectral peak list frames to an AutoAssign peak lists.
bmrbSPL2SparkyPks.pl - converts BMRB spectral peak list frames to Sparky peak lists.
bmrb2SparkyRL.pl - converts bmrb format to Sparky Resonance List format.
bmrb2XeasyRL.pl - converts bmrb assigned chemical shift save frames to Xeasy prot format.
bmrb_assign_spl.pl - assigns the spectral_peak_lists in a BMRB file.
bmrb_apply_shifting.pl - apply atom type shifting to the shifts of a bmrb file.
bmrb_calculate_shifting.pl - calculate difference in same shifts between two bmrb files.
bmrb_extract_shifts.pl - extract a list of shifts from a bmrb file.
cmap2bmrb.pl - converts a cmap file into a BMRB file.
compare_bmrb.pl - compares two bmrb files and returns how well they match.
concat_bmrb_shifts.pl - combine a set of bmrb files.
create_bmrb.pl - converts a list of shift assignments in 3 column format into a BMRB file.
jval2bmrb.pl - converts AutoStructure Input J HNHA values into BMRB coupling constants save frame.
manage_bmrb.pl - manage save frames inside a BMRB file.
missing_shifts.pl - reports the missing AtomTypes in a given BMRB file.
pks2bmrb.pl - Converts AutoAssign peak list into BMRB spectral peak list save frame.
sec2bmrb.pl - converts AutoStructure output .sec file into BMRB secondary_structure save frame.
sparkyPks2bmrb.pl - converts a sparky peaklist into a BMRB assigned peak list save frame.
sparkyRL2bmrb.pl - converts Sparky resonance list into a BMRB file.
1) Compare two BMRB files to see how assignments from two different samples differ.
The following command compares two BMRB files:
% compare_bmrb.pl data1.bmrb data2.bmrb -master -verbose -Ct 0.5 -Nt 0.5 -Ht 0.05This comparison makes the first BMRB the template or "master" chemical shift list to compare to.
This produces the following output:
(data2.bmrb) F4 - N 116.4 != 115.66,115.66 (data1.bmrb)This gives a report of those chemical shifts in the second BMRB file that differ from chemical shifts present in the first by amounts larger than the given tolerances.
(data2.bmrb) C14 - N 119.9 != 117.66,117.66 (data1.bmrb)
(data2.bmrb) C14 - H 8.66 != 8.605,8.605,8.5941 (data1.bmrb)
(data2.bmrb) C14 - CA 60.81 != 60.22 (data1.bmrb)
(data2.bmrb) K15 - HA 4.63 != 4.578 (data1.bmrb)
(data2.bmrb) I18 - N 125.6 != 125.06,125.06 (data1.bmrb)
(data2.bmrb) Y21 - N 115.1 != 115.66,115.66 (data1.bmrb)
(data2.bmrb) F22 - HA 5.49 != 5.438 (data1.bmrb)
(data2.bmrb) A27 - HA 4.41 != 4.468 (data1.bmrb)
(data2.bmrb) T32 - N 108.0 != 108.66,108.66 (data1.bmrb)
(data2.bmrb) T32 - HA 5.51 != 5.458 (data1.bmrb)
(data2.bmrb) K41 - HA 4.55 != 4.618 (data1.bmrb)
(data2.bmrb) N44 - HA 5.15 != 5.068 (data1.bmrb)
(data2.bmrb) K46 - CA 58.78 != 58.22 (data1.bmrb)
(data2.bmrb) E49 - N 117.4 != 119.56,119.56 (data1.bmrb)
(data2.bmrb) C51 - HA 1.76 != 1.878 (data1.bmrb)
(data2.bmrb) R53 - N 121.1 != 120.26,120.26 (data1.bmrb)
(data2.bmrb) R53 - HA 4.20 != 4.148 (data1.bmrb)
(data2.bmrb) C55 - HA 4.79 != 4.608 (data1.bmrb)
(data2.bmrb) G57 - HA 4.05 != 4.158,3.968 (data1.bmrb)
Comparison of data1.bmrb and data2.bmrb has 20 errors.
Comparison of data1.bmrb and data2.bmrb has 176 comparable shifts.
Master list data1.bmrb has 190 unused shifts.
2) Extract certain save frames from a BMRB file.
The following command shows which save frames are in the BMRB file:
% manage_bmrb.pl bmr4995.strThis produces the following output:
List of save frames in bmr4995.strThe following command extracts save frames 1, 19, 20, 11, 12, 13, 14, and 15 into a new BMRB file in that order:
----------------------------------
1) entry_information - entry_information
2) entry_citation - entry_citation
3) system_GlyTM1bZip - molecular_system
4) GlyTM1bZip - monomeric_polymer
5) natural_source - natural_source
6) experimental_source - experimental_source
7) GlyTM1bZip_ - sample
8) 15N-GlyTM1bZip - sample
9) 15N - sample
10) GlyTM1bZip_heterodimer - sample
11) VNMR - software
12) SPARKY - software
13) AutoAssign - software
14) AutoStructure - software
15) Dyana - software
16) NMR_spectrometer - NMR_spectrometer
17) NMR_applied_experiment - NMR_applied_experiment
18) conditions_1 - sample_conditions
19) chemical_shift_reference - chemical_shift_reference
20) chemical_shifts - assigned_chemical_shifts
21) GlyTM1bZip - coupling_constants
% manage_bmrb.pl bmr4995.str -extract 1,19,20,11,12,13,14,15 -output subset1.bmrbThe following command shows a list of save frames in the new BMRB file (subset1.bmrb):
% manage_bmrb.pl subset1.bmrbThis produces the following output:
List of save frames in subset1.bmrb
----------------------------------
1) entry_information - entry_information
2) chemical_shift_reference - chemical_shift_reference
3) chemical_shifts - assigned_chemical_shifts
4) VNMR - software
5) SPARKY - software
6) AutoAssign - software
7) AutoStructure - software
8) Dyana - software