1. I am using the old version of TraDES. Should I upgrade to TraDES-2?


First - Quality is improved: If you are doing Intrinsic Disorder sampling, there is a minor bug in the old version that causes atom-bounciness to degenerate over the length of the run, that means that some of the structures at the end of the run will have poor atom-atom distances, and we note that it can affect polymer statistics. This behavior was intended for near-neighbor sampling, and now has been disabled for default use.

Second - the software defaults are more reasonable, error-tracking is better handled (every executable has its own error log file), and there are lots of new features including the TraDES R Analysis package (attached source code at the bottom of the home page).  The file in the /Documentation/ folder "mapcommands" lists the differences between the old foltraj executable and the new trades executable.

Third - it is now open-source!  This is the list of the new executables:

Core Tools:
    benchtraj -   TraDES benchmarking and unit test - RUN THIS FIRST.
    seq2trj   -     Make *.trj files from FASTA
    str2trj   -      Make *.trj files from 3D structures in ASN.1 format
    trades    -     The TraDES sampling engine (formerly foldtraj)
    str2pdb  -     Convert ASN.1 files to PDB files (save space, use ASN.1!)
    strSummary - Reports on Asn.1 file contents, outputs FASTA, Ramachandran angles
                       NOTE - use strSummary for file compatibility inspection.
   
Analysis Tools: (Input ASN.1 3D files only)
    ramangL   - Output Ramachandran Angles for a set of *.val samples
    solvate   -   Add/remove solvent layers to an ASN.1 3D structure, and compute Phi/Psi & potentials.
    solvateL  -   Loop form of solvate for multi-file TraDES data postprocessing.

Higher-Order Assembly Tools: (For dock-by-alignment methods)
    salign    - Align ASN.1 structure, for movies or dock-by-alignment
    strMerge  - Merges two ASN.1 files - for dock-by-alignment methods
    crashchk  - Post-process steric collision testing code

Ensemble Movie Tools: (For Unfolding Pathways or Solvated Disorder Sets):
    bin2prt   - Convert ASN.1 binary structure to ASN.1 ascii (for movie making)
    concatmodels  - Movie making - concatenates ASN.1 ascii structures into one file.
    prt2bin   - Convert ASN.1 ascii to binary (form movie making)
    analyzeMovie  - Output a variety of graphs and collated data for movie files.


2. Sometimes, the foldtraj/trades program of TraDES seems to get infinitely stuck. Do you know why?

In the new version, you might find it more responsive to backtracking and less likely to get stuck.  It has some backtracking improvements that were made from Distributed Folding project that were not in the 2003 binaries.  If you are still having problems, remember getting stuck is a function of backtracking and running into a closed structure. This may be relieved by playing with the "atom bounciness" parameter, if there is a particular *.trj file that you are noticing a lot of "sticking" with.   

3. How do I convert a PDB file into a VAL file so that I can use one of the *.trj file making programs/scripts (maketrj, Unfoldtraj, Vistraj)

FIRST - STRIP out ALL HET groups from your PDB file and all solvent molecule (if your file has them already).
THEN Submit your PDB file to the VAST search service here:

http://structure.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html

The Service will offer you a page "Data Parsing Done"
at the bottom will be a button [View 3D Structure] of [All Atom Model] with Cn3D [Save File | See File | Display]
Select [Save File] and press the [View 3D Structure] Button

This will save a file called VS.c3d or VS.val depending on how yours system is configured.
This is a file is in Binary ASN.1 and it will be compatible with these programs - or you can load it into Cn3D to check it.

NOTE - This works for SINGLE Chain protein PDB files only.

4. COIL ONLY SAMPLING?  In the 2008 Paper - Conformational distributions of unfolded polypeptides from novel NMR techniques. Meier S, Blackledge M, Grzesiek S. J Chem Phys. 2008 128:052204.  the authors suggest that sampling with the COIL only components of PDB ramachandran space best match the NMR data from intrinsically unfolded domains.  How can TraDES generate COIL-only trajectory files?

You can make a COIL only *.trj file with the new TraDES-2 command:

seq2trj -f PolyYS_100.faa -o polyYS_100_coil -c

Also BETA only sampling is supported:

seq2trj -f PolyYS_100.faa -o polyYS_100_beta -b

And for 50% Beta, 50% COIL use both:

seq2trj -f PolyYS_100.faa -o polyYS_100_beta -c -b