| 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.
(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.
(in preparation?)
e-mail:
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