Input Files

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Basically you need the following data files in order to use smartnotebook.

• processed nmr data in "nv" format
• peaklists in "xpk" format
• sequence file in 3 letter code or a chemical shift file

A more detailed description now follows:

1. *.nv - These are your processed spectra files which nmrview uses for display. The configurations rules found in lib/experiments/triple-res assume atoms H,C,N for the x,y,z dimensions respectively. Also, the spectra are processed such that ca is a positive intensity, cb is negative. You can change these configuration files if you want but there are several files to change. It is much easier to process your spectra in the fashion outlined above.

2. *.xpk - These are your peakpick files which correspond with the processed spectra files above. Again, the atoms are specified in the order Hn C N.

3. sequence - This is your sequence in 3 letter code, one per line. This file is required if you do not have your own chemical shifts constraints file mentioned below.

4. shifts - Smartnotebook has no innate knowledge about how to map the chemical shifts suggested by your chain to residues in your sequence. It relies entirely on the integrity of a user-provided chemical shifts constraints file, and if one is not provided, to generate a default one (snb.out/shifts) using the simple program "makeshift" or the complex software "orb" where you provide homologous sequence shift files.

   The makeshift program is just like peakcon and nmrview, an independent piece of software that smartnotebook calls to perform a task. The program generates a chemical shifts constraints file based on the average shifts and standard deviations of the BMRB database (see lib/makeshift.bmrb) and on the naming conventions found in (lib/makeshift.def).

   If you plan to use "orb" then you are directed to the example case study provided. The advantage of custom chemical shift files is that it should allow users to arrive at an unambiguous assignable chain quicker, as homologous shift information is built into the constraint files.

   Tip: Not that I wish to dampen your enthusiasm for creating your own chemical shift files, just keep in mind that having more accurate peakpick files *may* be better investment of your time within smartnotebook.

5. ppm.out - If you have previous assignments, then smartnotebook can form suggested chains from this data. This would be interesting if you have assignments which are computer generated and you wish to verify the corresponding chains with your spectra.

6. chains.suggest - Same as ppm.out except the format is a chains file. Third party software may find it easier to format its results in this format as opposed to ppm.out.

Unless you change the default configuration, smartnotebook will use snb.out as the directory which defines the current program state. Here is a summary of the output files which are maintained here.
1. *.xpk - These should be your original peakpick files plus any folded peaks plus any added assignments you made from using smartnotebook. These files are updated whenever you assign or un-assign a chain or change the folded peaks information.

2. *.fold - These files which correspond with the peakpick files contain entries which override peakpick file entries. Whenever you change the designation of a folded peak within smartnotebook, these files get updated.

   Tip: Try to process your folded peaks before creating chains.

3. chains - This file keeps track of all the chains you have created. Any command which causes a change to the chains will automatically update this file. The "chains" file is your most important output file because snb can re-create your session from this file! Backups of this file are constantly written to the log file.

4. con.peakcon.* - These are the very important connection output files that smartnotebook reads to find relationships between peaks. The "*" in the filename represents the type of pattern that the connection file contains, "peakcon" is the program that created it, and "con" is the prefix that tells smartnotebook that this is a connection file. These files are created at startup of snb and they will not be updated unless you modify the input peakpick files. One of the reasons you may modify the input peakpick files is because you discover a missing peak.

   With this is mind, you should place any custom built connections into a file where the "peakcon" in "con.peakcon.*" is replaced with your own program/method for finding connections. If you replace "*" with your own unique pattern identifier, you will be able to distinguish these in the connection panel. For formatting purposes, keep your pattern identifier to less than 5 letters.

   The format of the connection fields can vary with the types of spectra and atom shifts we are interested in. The configuration files (eg lib/hsqc/hsqc-1) and the rules files (eg lib/hsqc/rules.dxx.00) must agree on what the data format of a pattern record looks like.

5. snb.log - This is a verbose log file of your smartnotebook session.

6. ppm.out - These are your assignments in "ppm.out" format. This file is updated whenever you assign or un-assign a chain.

7. shifts - This is the default chemical shifts constraints file as created by "makeshift".

8. VERSION - The version of smartnotebook which created this output directory, useful in diagnosing compatibility issues with future versions of smartnotebook.

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