X-PLOR v3.843: A System for X-ray Crystallography and NMR

General Information

X-PLOR may be used to 'MODEL' structures such that they do not violate experimentally derived parameters, such as dihedral angles and distances between atoms.

 

  • Executables

    xplor: The actual program

    cdih_make: Generates RNA/DNA dihedral angles from an input sequence

    dm: Calculates 1H-1H distances in .pdb files

    noe_in: Generates noe.dat files from dm output

    cdih_measure: Measures heavy atom dihedral angles from .pdb files

     

  • X-PLOR input script files

    build.inp: Generates a *.psf structure file

    template.inp: Generates a *.pdb structure file

    dg.inp: Generates a distance geometrized structure

    dgsa.inp: Performs a simulated annealing

     

  • Libraries

    dna-rna-allatom.par: parameter file

    dna-rna-allatom.top: topology file

    Comparison of parameter and topology files

     

  • Restraint files

    cdih.dat: Dihedral angles file

    noe_std.dat: Standard NOE distances file

    noe_exp.dat: Experimentally derived distances file

    noe_hbond.dat: Basepairing NOEs

    planar.dat: Nucleotide base pair planarity file

    Restraint files

    There are three main restraint files needed, one for all your distance (noe_*.dat) information, one for your dihedral (cdih_*.dat) information and one for forcing planarity between basepairs (planar.dat).

    Distance information (noe_*.dat) files

    For the sake of keeping things easier to track, I usually break my NOE file into three files. The first, noe_hbond.dat, contains distance information to force basepairing. The second, noe_std.dat, contains "standard" distances to force A-form structure (in the case of RNA), this information is not derived from experiment. The third is noe_exp.dat and contains any experimentally derived distance information you may have.

    Making the the noe_std.dat file:
    This file can be built by first generating a .pdb file from Insight95 which contains the standard structure elements, running i2x file_i.pdb > file_x.pdb to make an X-PLOR compatible pdb file, running dm file_x.pdb > dist.txt to make a table of standard distances and finally converting this to an X-PLOR restraint file with noe_in dist.txt > noe_std.dat.

    Making the the noe_std_a.dat and noe_std_b.dat files for duplex DNA:
    These files can be generated in a similar manner to the noe_std.dat file. Use Insight95 to generate a .pdb file for each strand in the duplex: file_a_i.pdb and file_b_i.pdb. Then run i2x file_a_i.pdb > file_a_x.pdb and i2x file_b_i.pdb > file_b_x.pdb. Run dm file_a_x.pdb > dist_a.txt and dm file_b_x.pdb > dist_b.txt. Now run noe_in dist_a.txt > noe_std_a.dat and noe_in dist_b.txt > noe_std_b.dat. And now, and this is VERY IMPORTANT, you must edit the noe_std_a.dat and the noe_std_b.dat files. For noe_std_a.dat, edit all statements that say "resid" to say "segid a and resid". For noe_std_b.dat, edit all statements that say "resid" to say "segid b and resid". It's that simple!

    Making a seq_rna or seq_dna "sequence" file:
    These files are made in order to ease your pain in generating the cdih.dat, noe_hbond.dat, and planar.dat files. They are descibed in a little more detail below. Here is a typical seq_rna and here is a typical duplex seq_dna file.

    Making the noe_hbond.dat file:
    If you have a perfect anti-parallel base-paired duplex DNA, you should run noe_hbond_make seq_dna > noe_hbond.dat . This will generate all of the H-bond constraints for a fully paired duplex. If you do not have a standard duplex, you can run this program and edit the output, or you can:

    Cut and paste these standard values for RNA

    ! A1-U4 Watson-Crick (A-form RNA)
assign (segid A and resid  1 and name N1 ) (segid B and resid  4 and name H3 )  1.93 0.20 0.20
assign (segid A and resid  1 and name N1 ) (segid B and resid  4 and name N3 )  2.95 0.20 0.20
assign (segid A and resid  1 and name N6 ) (segid B and resid  4 and name O4 )  2.83 0.20 0.20
assign (segid A and resid  1 and name H62) (segid B and resid  4 and name O4 )  1.82 0.20 0.20  
! U2-A3 Watson-Crick (A-form RNA)
assign (segid A and resid  2 and name H3 ) (segid B and resid  3 and name N1 )  1.93 0.20 0.20
assign (segid A and resid  2 and name N3 ) (segid B and resid  3 and name N1 )  2.95 0.20 0.20
assign (segid A and resid  2 and name O4 ) (segid B and resid  3 and name N6 )  2.83 0.20 0.20
assign (segid A and resid  2 and name O4 ) (segid B and resid  3 and name H62)  1.82 0.20 0.20  
! G3-C2 Watson-Crick (A-form RNA)
assign (segid A and resid  3 and name H1 ) (segid B and resid  2 and name N3 )  1.89 0.20 0.20
assign (segid A and resid  3 and name N1 ) (segid B and resid  2 and name N3 )  2.91 0.20 0.20
assign (segid A and resid  3 and name H22) (segid B and resid  2 and name O2 )  2.08 0.20 0.20
assign (segid A and resid  3 and name N2 ) (segid B and resid  2 and name O2 )  3.08 0.20 0.20
assign (segid A and resid  3 and name O6 ) (segid B and resid  2 and name H42)  1.71 0.20 0.20
assign (segid A and resid  3 and name O6 ) (segid B and resid  2 and name N4 )  2.72 0.20 0.20
! C4-G1 Watson-Crick (A-form RNA)
assign (segid A and resid  4 and name N3 ) (segid B and resid  1 and name H1 )  1.89 0.20 0.20
assign (segid A and resid  4 and name N3 ) (segid B and resid  1 and name N1 )  2.91 0.20 0.20
assign (segid A and resid  4 and name O2 ) (segid B and resid  1 and name H22)  2.08 0.20 0.20
assign (segid A and resid  4 and name O2 ) (segid B and resid  1 and name N2 )  3.08 0.20 0.20
assign (segid A and resid  4 and name H42) (segid B and resid  1 and name O6 )  1.71 0.20 0.20
assign (segid A and resid  4 and name N4 ) (segid B and resid  1 and name O6 )  2.72 0.20 0.20
    Cut and paste these standard values for B-form DNA
    ! A1-T4 Watson-Crick (B-form DNA)
assign (segid A and resid  1 and name N1 ) (segid B and resid  4 and name H3 )  1.92 0.20 0.20
assign (segid A and resid  1 and name N1 ) (segid B and resid  4 and name N3 )  2.95 0.20 0.20
assign (segid A and resid  1 and name N6 ) (segid B and resid  4 and name O4 )  2.81 0.20 0.20
assign (segid A and resid  1 and name H62) (segid B and resid  4 and name O4 )  1.78 0.20 0.20  
! T2-A3 Watson-Crick (B-form DNA)
assign (segid A and resid  2 and name H3 ) (segid B and resid  3 and name N1 )  1.92 0.20 0.20
assign (segid A and resid  2 and name N3 ) (segid B and resid  3 and name N1 )  2.95 0.20 0.20
assign (segid A and resid  2 and name O4 ) (segid B and resid  3 and name N6 )  2.81 0.20 0.20
assign (segid A and resid  2 and name O4 ) (segid B and resid  3 and name H62)  1.78 0.20 0.20  
! G3-C2 Watson-Crick (B-form DNA)
assign (segid A and resid  3 and name H1 ) (segid B and resid  2 and name N3 )  1.89 0.20 0.20
assign (segid A and resid  3 and name N1 ) (segid B and resid  2 and name N3 )  2.91 0.20 0.20
assign (segid A and resid  3 and name H22) (segid B and resid  2 and name O2 )  1.98 0.20 0.20
assign (segid A and resid  3 and name N2 ) (segid B and resid  2 and name O2 )  3.01 0.20 0.20
assign (segid A and resid  3 and name O6 ) (segid B and resid  2 and name H42)  1.67 0.20 0.20
assign (segid A and resid  3 and name O6 ) (segid B and resid  2 and name N4 )  2.70 0.20 0.20
! C4-G1 Watson-Crick (B-form DNA)
assign (segid A and resid  4 and name N3 ) (segid B and resid  1 and name H1 )  1.89 0.20 0.20
assign (segid A and resid  4 and name N3 ) (segid B and resid  1 and name N1 )  2.91 0.20 0.20
assign (segid A and resid  4 and name O2 ) (segid B and resid  1 and name H22)  1.98 0.20 0.20
assign (segid A and resid  4 and name O2 ) (segid B and resid  1 and name N2 )  3.01 0.20 0.20
assign (segid A and resid  4 and name H42) (segid B and resid  1 and name O6 )  1.67 0.20 0.20
assign (segid A and resid  4 and name N4 ) (segid B and resid  1 and name O6 )  2.70 0.20 0.20
    Making the planar.dat file:
    Once again, if you have a regular double helix, you should take advantage of your seq_dna file by running planar_make seq_dna > planar.dat. This will give you the planarity restraints for base-pairs.

    Making the noe_exp.dat file:
    There is no easy way of generating this file, you have to edit by hand, use the other noe files as a guide.

    Dihedral information (cdih.dat) files

    Unlike the NOE information, I use a single dihedral angle file, cdih.dat which contains both the experimentally derived angle information and any standard angle information.

    Making the cdih.dat file:
    This can be easily generated by editing a "sequence" file (I call mine seq_*) appropriately, and using cdih_make to generate the cdih.dat file. Both your standard angle info and experimentally derived angle info can go into the "sequence" file.

    Here is an example of a seq_rna file which is used to generate a 13 nucleotide RNA hairpin: seq_rna. cdih_make seq_rna > cdih.dat generates the file. Notice that the RNA has sequence 5'-AACAGUUUCUGUU-3' and that standard dihedral angles are applied to A1-A4 and U10-U13. No dihedral restaints are applied to G5 and C9. Specific non-standard dihedral angles are given to U11-U12.

    Here is an example of a double strand DNA using segment IDs seq_atgc. cdih_make seq_atgc > cdih.dat generates the file. Notice that You must use 'segids' for multi strand molecules.

    Use this header when starting your own seq_* files seq_header. Just remove one of the two default values listed.

    RNA Tutorial: AUGC single strand

    Here is a quick tutorial which will walk you through generating a simple RNA using standard A-form structural information.

    Make a ~/xplor/augc/ directory and copy all the AUGC sample files there (cp /usr/local/lib/xplor/augc/* .). The sample files contain the information to build the quadnucleotide single strand RNA, AUGC, used as an example.

    NOTE: Before you rerun a process from the beginning, delete any *.out, *.pdb and *.rsf files from your working directory. Things get named strangely and/or get appended to if these files exist.

    First: Generate the build.rsf and template.pdb structure files

    If completed successfully, the .pdb file may be viewed (midas build.pdb). It should appear as a single strand of RNA with randomly positioned nucleotides, with the correct sequence.

    Second: Create (edit) the NOE constraint files.

    Third: Create (edit) the Dihedral angle constraint files.

    Fourth: Do distance geometerization and embedding (vector to atomic) and simulated annealing

    View the output dgsa.??.pdb files (midas dgsa.??.pdb) They should look like good RNA structure. These output .pdb files can also be examined by running them through the program cdih_measure (cdih_measure file.pdb).