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Support for BCL::EMFold Software
Technical support is available throughout the license period.
For scientific or technical questions related to BCL::EMFold, please contact us.
If there is a major bug fix or significant improvements to the application, entities with current licenses will be notified via email and will be given access to the updated software.
Installation Procedures
BCL::EMFold
Copy the appropriate executable into the respective directory on your PC. No additional steps are required for installation. If there are major bug fixes or revisions, an email will be sent out to entities with current licenses so that the newest application can be installed.
Running BCL::EMFold
HOW TO RUN THE APPLICATION
Running BCL::EMFold consists of five main steps.
1.) Create the fasta sequence file for the protein to be studied. You will need the protein sequence in fasta format, and it should be stored in a <.fasta> file. An example is given below. For more information about fasta formats, please visit http://www.ncbi.nlm.nih.gov/blast/fasta.shtml.
2.) Create the pool file. This could be done by hand or using the CreatePool application in the BCL. An example is given below.
3.) Create the body restraint file. This is just like a pdb file containing helix coordinates wherever density rods are observed in the density map. An example is given below.
4.) Create the score file. Simply use the example that is given below.
5.) Run BCL::EMFold. At a command prompt, navigate to the location of your BCL::EMFold executable program. The syntax for running the application looks like the following:
bcl_emfold.exe Fold -nmodels 1 -fastas XXXXA.fasta -pool XXXX.pool -mc_number_iterations 2000 500 -mc_temperature_fraction 0.25 0.05 -prefix ./pdbs/ -body_restraint XXXX.cst_body 500 1.0 1.0 2.0 2.0 -1.0 true -random_seed -message_level Critical -score_weightset weights_assembly.score
BCL::EMFold needs a fasta sequence with the extension <.fasta>, a pool file <.pool>, a constraints file <.cst_body> and a score weightset file <.score> to exist in the same directory.
FLAGS
-nmodels 1
Number of models that a single run creates (1 in that case)
-fastas XXXXA.fasta
The fasta file containing the sequence of the protein.
-pool XXXX.pool
The pool file containing the secondary structure prediction of the protein.
-body_restraint XXXX.cst_body 500 1.0 1.0 2.0 2.0 -1.0 true
The file containing the restraints extracted from the density map, the weight for the occupancy score, and parameters describing the shape of the potential used in the occupancy score.
-score_weightset weights_assembly.score
The score file detailing which scores to use.
-mc_number_iterations 2000 500
The number of total steps (2000) as well as rejected steps in a row (500) before the Monte Carlo search is stopped.
INPUT AND OUTPUT.
BCL::EMFold requires four inputs, a) a fasta file, b) a pool file, c) a restraints file and d) a score file.
a) The fasta file uses one letter codes for protein sequence and looks
like the following:
>1UBI:A|PDBID|CHAIN|SEQUENCE MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
b) The pool file specifies the predicted secondary structure elements and looks like the following:
bcl::assemble::SSEPool HELIX 1 1 TRP A 4 ALA A 19 16 HELIX 2 2 TRP A 4 LEU A 36 33 HELIX 3 3 LYS A 5 GLU A 18 14 HELIX 4 4 LYS A 5 SER A 33 29 HELIX 5 5 LYS A 7 THR A 22 16 HELIX 6 6 GLU A 20 SER A 33 14 HELIX 7 7 LEU A 21 LEU A 36 16 HELIX 8 8 LEU A 41 TRP A 51 11
c) The restraint file encodes the density rods as helices and looks like the following:
SEQRES 1 A 152 PRO PRO LYS TRP LYS VAL LYS LYS GLN LYS LEU ALA GLU SEQRES 2 A 152 LYS ALA ALA ARG GLU ALA GLU LEU THR ALA LYS LYS ALA SEQRES 3 A 152 GLN ALA ARG GLN ALA LEU SER ILE TYR LEU ASN LEU PRO SEQRES 4 A 152 THR LEU ASP GLU ALA VAL ASN THR LEU LYS PRO TRP TRP SEQRES 5 A 152 PRO GLY LEU PHE ASP GLY ASP THR PRO ARG LEU LEU ALA SEQRES 6 A 152 CYS GLY ILE ARG ASP VAL LEU LEU GLU ASP VAL ALA GLN SEQRES 7 A 152 ARG ASN ILE PRO LEU SER HIS LYS LYS LEU ARG ARG ALA SEQRES 8 A 152 MET LYS ALA ILE THR ARG SER GLU SER TYR LEU CYS ALA SEQRES 9 A 152 MET LYS ALA GLY ALA CYS ARG TYR ASP THR GLU GLY TYR SEQRES 10 A 152 VAL THR GLU HIS ILE SER GLN GLU GLU GLU VAL TYR ALA SEQRES 11 A 152 ALA GLU ARG LEU ASP LYS ILE ARG ARG GLN ASN ARG ILE SEQRES 12 A 152 LYS ALA GLU LEU GLN ALA VAL LEU ASP HELIX 1 1 PRO A 2 SER A 33 1 32 HELIX 5 5 GLY A 67 ARG A 79 1 13 HELIX 6 6 SER A 84 ARG A 97 1 14 HELIX 8 8 SER A 123 ASP A 152 1 30 ATOM 8 N PRO A 2 -34.913 10.141 21.737 1.00 45.99 N ATOM 9 CA PRO A 2 -34.039 10.544 20.632 1.00 46.41 C ATOM 10 C PRO A 2 -32.544 10.299 20.814 1.00 47.36 C ATOM 11 O PRO A 2 -32.078 9.922 21.893 1.00 48.61 O ATOM 12 CB PRO A 2 -34.341 12.030 20.469 1.00 45.93 C ATOM 13 CG PRO A 2 -35.724 12.173 21.015 1.00 46.71 C ATOM 14 CD PRO A 2 -35.693 11.293 22.226 1.00 46.13 C ATOM 15 N LYS A 3 -31.807 10.533 19.730 1.00 47.24 N ....
d) The score file specifies used scores and should look like the following:
bcl::storage::Table nr co rgyr aadist aasmooth aaneigh aavmd aanvec annsasa aaols loop ssepack_fr strand_fr sum rmsd rmsd100 weights 0 0 0 0 0 0 0 0 0 0 265 0 0 0 0 0
Column descriptions and score weights should be in one line respectively!
