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loop is a top level plop command that will initiate loop prediction and related subcommands in Plop. Generally, the loop command is followed by one of the sub-commands listed below and the loop bounds in standard Plop residue format. For example:

 loop predict A:10 A:15 [ options ]

predicts the loop from residue A:10 to A:15.


[edit] loop find

[edit] loop sample

[edit] loop contact

"contact," as in energy

[edit] loop predict

Begins a single loop prediction run. If the loop includes a helix that will be built, the helix_build command and the first and last helix residues must be specified immediately following the loop predict A:10 A:15 command. For example:

 loop predict A:10 A:25 helix_build A:12 A:18

[edit] loop validate

Similar to loop predict...

[edit] loop mc

Loop Monte Carlo

[edit] loop quality

[edit] loop surroundings

List the residues surrounding a set of predicted loops. Expects the sidecut option. For example:

 loop surr A:10 A:15 sidecut 7.5

This command will perform an initial backbone buildup and list all residues within 7.5 angstroms from the initial set of loops. No clustering or side optimization is carried out after the buildup.

[edit] loop score

Performs an energy calculate on the protein after loading loop residues and associated rotamer libraries, so that any pseudo-energy terms related to loop rotamers can be included in the energy calculation.

[edit] Options

 add_clust yes/no    -
 alt_rms_intvl       - alternative loop bounds to use for RMSD calculation only
 alt_scoring_intvl   - alternative loop bounds to use for loop-based scoring only
 ana yes/no          - analytical closure
 angcut              -
 angcut_auto         -
 backmin yes/no      -
 buried              -
 check_with_segment  - checks phi, psi against the dipeptide library independent of library used to sample 
 cling               -
 clust               -
 clust_atom          -
 concut              -
 constrain           - cartesian constraint to within x angstrom of a fixed point
 eclust              -
 exposed             -
 failsafe yes/no     -
 ideal yes/no        - 
 longloop            -
 loopfile            -
 maefile             -
 maxangdev           - constrain dihedral to within x degrees of starting
 maxcalpha           - cartesian constraint to within x angstrom of starting
 maxhelixdev         - constrain dihedral to within x degrees of ideal helix
 maxstranddev        - constrain dihedral to within x degrees of ideal strand
 mc                  - set mc params
 membrane            -
 mid_loop            -
 mid_move            -
 midrescons          -
 min                 - set min params
 mpass               - 
 native_opt yes/no   - minimize & side opt on native
 nclust              -
 nclust_stage        -
 nconf_init          - 
 nconf_min           -
 niter               -
 niter_side          -
 nonstan back/side   -
 noscoptfile         -
 nres_stage          -
 ofac                - overlap factor; default = 0.65
 omega               -
 pdbfile             -
 perturb_angle       - perturb option in analytical closure
 perturb_level       - perturb option in analytical closure
 rand                -
 rmsdfile            -
 rmsdtype            - user-specified RMSDs in addition to defaults. Requires align and/or rmsd keyword,
                       e.g., "rmsdtype align calpha A:1 A:5 rmsd A:2 A:4"
                       or    "rmsdtype rmsd ncaco A:2 A:4" (global alignment)
 segment yes/no      - default to dipeptide library for loops > 13 residues, or LHL halves > 6 residues.
 side1               -
 side2               -
 sideadd             - add a list of additional residues 
 sidecut             -
 sidefrz             - 
 sideres             -
 statrmsd yes/no     -
 summfile            -
 tether              -
 tree_verb           -

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