RNABC manual Home Page: Richardsons' Laboratory Xueyi Wang - 6/2006

RNABC syntax:

rnabc [-Flags [value]] filename

Filename should be in pdb file format and the result writes to standard output in kinemage file format.

For example, if we want to correct the suite 76-77, chain 9 in 1S72, and write the results to a kinemage file, then the command line is:

rnabc -RESNUM77 -CHAIN9 -SIG3 1S72.pdb > 1S72_9_77.kin

Flags available:

-RESNUM#                 To fix clashes in a suite, give the number of the 
                         residue containing the phosphorus.
                         (default = 
                         the first residue containing a phosphorus atom)
-CHAIN#                  The chain ID
                         (default = the first chain)

-MODEL#                  The model ID
                         (default = the first model)

-ALTLOC#                 Which Alternative location to choose, if the pdb has 
                         alternative locations for atoms.
                         (default = ' ')

-PUCKER#[-#][-#]         Specific pucker types of the first and second sugars 
                         in suite.
                         For clash in residue, there is only one sugar pucker. 
                         0 - determined by the perpendicular distance from
                             phosphate to first base.
                         1 - determined by the perpendicular distance from
                             phosphate to bond N1/9 - C1* 
                         2 - C2* endo pucker 
                         3 - C3* endo pucker 
                         4 - original sugar pucker.

-COURSESTEP#             Span of degrees in coarse step. (default = 5.0)

-FINESTEP#               Span of degrees in fine step. (default = 1.0)
-PHOSPHORUS #.# #.# #.#  Adjust position of "central" phosphorus in a suite, 
                         the x axis is defined as from C1* in first base to C1*
                         in second base. By defining triangle P-C1*(1)-C1*(2)
                         counterclockwise, the z axis points out of the triangle
                         and is perpendicular to it.

-FIRSTBASE #.# #.# #.#   Adjust the position of first base using the same
                         coordinate system in -PHOSPHORUS.

-SECONDBASE #.# #.# #.#  Adjust the position of second base using the same
                         coordinate system in -PHOSPHORUS.

-PARAMETER# [file]       Specify the set of bond lengths and angles
                         1 - canonical parameters
                         2 - the original bond lengths and angles in suite 
                         4 - the average of 1 and 2 
                         8 - user defined parameters 
                         Different sets can be used at the same time, 
                         e.g. 7 means calculating the structure three times, 
                         each time use one set of parameters from 1, 2 and 4.

-SIG#                    The allowable range of the bond angles in sugar puckers
                         in multiples of the standard deviation sigma value of 
                         each bond angle (default=3).
-OUTPUTPARAMETER [file]  Output the parameter sets currently used in the program.

-ENERGYFUNC#.#           Energy function used for checking bad clashes
                         If designated by number, e.g. default=0.4,
                         means the function is vdwi+vdwj-0.4. Otherwise, 
                         new energy function must be specified (unavailable).
-HBOND#.#                Hydrogen bonds distance checking bad clashes.
                         (default=0.6 Angstrom)

-WITHINCHAIN             Check collisions with only the atoms on the local chain

-HET                     Consider steric clashes with HET atoms

-WATER                   Consider steric clashes with water molecules

-ALL                     Consider steric clashes with HET atoms, water molecules
                         and atoms on the other chains

-CONFORM#                Cluster and output the results.
                         # - number of middle conformations to output, or 
                         A - Output the conformations closest to the 42
                             conformations defined by the Richardson Lab.
                         B - Output the conformations closest to the 42
                             conformations defined by the Richardson Lab, 
                             and the ranges for dihedrals given by Laura Murray.
-NOMEASUREDIHEDRAL       Not to measure dihedrals for each conformation.

-NOMEASURECONFORM        Not to determine conformation type for each 

-SHOWBALL                Show heavy atoms as balls in the output kinemage file.

-HELP                    Show all the command-line parameters.


(in preparation?)

Xueyi Wang <xwang AT cs DOT unc DOT edu>, or
David C. Richardson <dcr AT kinemage DOT biochem DOT duke DOT edu>
URL: http://kinemage.biochem.duke.edu
Biochemistry Department
Duke University
Durham, NC USA 27710