|RNABC manual||Home Page: Richardsons' Laboratory||Xueyi Wang - 6/2006|
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
-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. (default=1). 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 (default=1) 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 (default=0.4). 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. (default=10) # - 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 conformation. -SHOWBALL Show heavy atoms as balls in the output kinemage file. -HELP Show all the command-line parameters.
Xueyi Wang <xwang AT cs DOT unc DOT edu>, or
David C. Richardson <dcr AT kinemage DOT biochem DOT duke DOT edu>
Durham, NC USA 27710