RNABC (RNA Backbone Correction) is designed for reducing
the steric clashes in the backbone of existing RNA structures. It first fixes
the phosphate and base positions, which are the clearest parts in X-ray crystallography
structure, and then reconstructs the suite (from base to base) using forward
kinematics to fit the remaining atoms. The input parameters, like bond lengths,
bond angles and sugar pucker types, are from canonical values or specified by
users. The output results cluster the possible conformations that can be
constructed without steric clashes.
RNABC is created by Xueyi Wang and Prof. Jack Snoeyink at Department of Computer Science, University of North Carolina at Chapel Hill,
with the collaboration of the Richardson
Lab.
If you have any questions or suggestions for RNABC, please email to xwang@cs.unc.edu.
Xueyi Wang, Gary Kapral, Laura Murray, David Richardson, Jane Richardson, and Jack Snoeyink. (2007) RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone, Journal of Mathematical Biology, (pdf)
Talk in SIAM MI 2005: SIAM_MI2005_topology.ppt
Program: RNABC_win_0.95.zip (Windows)
RNABC_linux_0.95.zip (Linux)
Source code: source_win_0.95.zip (Visual C++ 6.0)
source_linux_0.95.zip (C++)
The RNABC uses the following format:
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, the command line is:
RNABC -RESNUM77 -CHAIN9 -SIG3 1S72.pdb > 1S72_9_77.kin
| The detailed descriptions of flags are: | ||
| -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 are 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. | |