Miscellaneous commands:

[1] nvseq ?infile? ?outfile?
Convert protein sequence format for NMRView. The input file should be in single-letter format. For example, 'nvseq seqfile.txt seqfile.seq'

[2] hsearch ?ChemicalShift?
search 1H CS in AssignPanel, for example, 'hsearch 5.0'

[3] nsearch ?ChemicalShift?
search 15N CS in AssignPanel, for example, 'nsearch 120.0'

[4] csearch ?ChemicalShift?
search 13C CS in AssignPanel, for example, 'csearch 30.0'

[5] aa ?AAname?
Search and display all the specified AA with assigned/unassigned atoms indicated by green/red color.
For example, 'aa w' or 'aa trp' . Click the button to display the corresponding slice in NOE spectrum.

[6] hsqclabel ?DatasetName? ?PeaklistName?
This command will create a new peaklist (specified by PeaklistName) for 1H-15N HSQC. The new peaklist will be labelled by residue name and number according to your backbone(N,HN) assignment in AssignPanel and be displayed in the HSQC spectrum.
For example, 'hsqclabel hsqc.nv hsqc_label.xpk'.
NOTE: If the peaklist already exists, the old one will be overwritten by this new one!

[7] ch3label ?DatasetName? ?PeaklistName?
This command will create a new peaklist (specified by PeaklistName) for 1H-13C HSQC. The new peaklist will be labelled by residue name,number and atom name according to your CH3 assignment in AssignPanel and be displayed in the 1H-13C HSQC spectrum.
For example, 'ch3label chsqc.nv ch3_label.xpk'.
NOTE: If the peaklist already exists, the old one will be overwritten by this new one!

[8] calcnoe ?NOERestraintFile?
Caculate NOE number, including intra, sequential, medium range and long range NOE. The results will be displayed in NMRView Console and be saved into "NOE_statistics.txt" file in the current working directory as well.
For example: 'calcnoe xxx.upl'

[9] totalassi
Caculate the total assigned atoms (CiHi,NiHi),exclusive of CO and other heavy atoms without protons attached.

[10]-1 calccacb
Caculate (CAassi-CAcoil)-(CBassi-CBcoil) for secondary structure predication. The result will be saved into "cacb.txt" file in the current working directory.

[10]-2 calccacb2 ?residue_num1? ?residue_num2?
This command is used for a protein with one disulfide bond. The two cysteine residue numbers are defined by residue_num1/2.
For example: 'calccacb2 10 25'.The result will be saved into "cacb.txt" file in the current working directory.

[11] talos2cns ?TalosFile? ?Count?
This command will extract dihedral angle constraints (except G or P) from TALOS prediction file for structural calculation in CNS or CYANA. The result file, dihed.tab, will be saved into the current working directory.
For example: 'talos2cns pred.tab 5'. This example will extract the angle restraints in "GOOD" class or with a "COUNT" number larger than or equal to 5. If you only want to extract "GOOD" prediction, set the "COUNT" number to 11.

[11] talos2cns ?TalosFile? ?Count?
This command will extract dihedral angle constraints (except G or P) from TALOS prediction file for structural calculation in CNS or CYANA. The result file, dihed.tab, will be saved into the current working directory.
For example: 'talos2cns pred.tab 5'. This example will extract the angle restraints in "GOOD" class or with a "COUNT" number larger than or equal to 5. If you only want to extract "GOOD" prediction, set the "COUNT" number to 11.

[12] talos2cyana ?TalosFile? ?Count?
This command will extract dihedral angle constraints (except G or P) from TALOS prediction file for structural calculation in CYANA. The result file, dihed.aco, will be saved into the current working directory.
For example: 'talos2cyana pred.tab 5'. This example will extract the angle restraints in "GOOD" class or with a "COUNT" number larger than or equal to 5. If you only want to extract "GOOD" prediction, set the "COUNT" number to 11.

[13] cali3dpeak ?OldPeaklist? ?NewPeaklist? ?x_ppm? ?y_ppm? ?z_ppm?
Use this command to calibrate the center position of the peaks in any 3D peak list. You should save the peaklist file first before use this command.
For example: 'cali3dpeak noesy.xpk noesy_cali.xpk 0.02 -0.01 0.25'. The new peaklist file will be saved into the current working directory.

[14] cali4dpeak ?OldPeaklist? ?NewPeaklist? ?x_ppm? ?y_ppm? ?z_ppm? ?z2_ppm?
Use this command to calibrate the center position of the peaks in any 4D peak list. You should save the peaklist file first before use this command.
For example: 'cali4dpeak 4dnoesy.xpk 4dnoesy_cali.xpk 0.02 -0.3 0.25 0.03'. The new peaklist file will be saved into the current working directory.

[15] sparky2nv ?SparkyCSFile?
Convert Sparky chemical shift file to NMRView format (ppm.out). "ppm.out" file will be saved into the current working directory.
For example: 'sparky2nv shifts.txt'

[16] addpeak
Add a peak to a 2D/3D/4D spectrum, centered at crosshair1 and cornered at crosshair2
For example: 'addpeak'
This command will not add intensities or volumes. use "Assign->Peaks->Int" to get peak Int. & vol.

[17] expk ?peaklistfile1? ?peaklistfile2?
Extract assigned peaks from a peaklist file (.xpk) into a new peaklist file, which is then loaded into into NMRView
For example: 'expk noesy.xpk temp.xpk'

[18] calcdist ?PDB_File? ?Residue_Number? ?Proton_Name? ?Distance?
In a PDB file (given as the first argument), find all pairs of protons (one of the two atoms is given as the second & third arguments) that have a distance smaller or equal to the one give as the last argument.
For example, 'calcdist test.pdb 1 HA 5.0'
Partial proton name is also acceptible. e.g. 'calcdist test.pdb 1 H 5.0'

[19] expdb ?PDB_File?
Extract each structure from a PDB file containg multi-structures.
e.g. 'expdb test.pdb'

[20] exlongnoe ?upper_limit_File?
Extract all the long-range NOEs from a upper-limit file (or any other NOE restraint file) and generate one txt file containing all long-range NOEs and another Macro file (Molmol) for labelling all these longe-range NOEs in a structure. The default names are longnoe.txt and longnoe.mac
For example, 'exlongnoe test.upl'

[21] calinoe
Calibrate NOE distances into 3 or 4 ranges based on intensity or volume. The input file should be a standard upper limit file generated by NMRView.

[22] ppmout ?Residue_Number"
Change residue number in ppm.out. Please make sure that ppm.out file is in the current working folder.
A new file, ppm.out.new, will be created in the same working folder.
For example, 'ppmout -6'. This command decreases each residue number by six.

[23] newcyana
Reformat seq, upl and lol files generaged by NMRView for structural calculation in CYANA2 or higher versions. Oxidized Cys residues (involved in disulfide bridges) and cis Pro can also be changed. Three new files with "_new" will be created in the current working directory.
NOE: The file name without extension saved from NMRView.
CYSS: Residue numbers of oxidized Cys. The numbers should be separated by space. For example, '12 34'
cPro: Residue numbers of Pro in cis form. The numbers should be separated by space. For example, '3 9 34'