.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.4.
.TH KING-PROBE "1" "September 2015" "king-probe 2.13.110909-1" "User Commands"
.SH NAME
king-probe \- Evaluate and visualize protein interatomic packing
.SH DESCRIPTION
Syntax: probe input.pdb >> out.kin
.IP
or: probe [flags] "src pattern" ["target pattern"] pdbfiles... >> out.kin
.SS "Flags:"
.TP
\fB\-SElf\fR
self intersection:   src  \-> src (default)
.TP
\fB\-Both\fR
intersect both ways: src <=> targ
.TP
\fB\-ONce\fR
single intersection: src  \-> targ
.TP
\fB\-OUt\fR
external van der Waals surface of src (solvent contact surface)
.TP
\fB\-AUTObondrot\fR filename
read and process an autobondrot file
.IP
shortcuts:
.IP
<<NO FLAGS>>same as: \fB\-4H\fR \fB\-mc\fR \fB\-het\fR \fB\-self\fR "altA ogt33"
.TP
\fB\-DEFAULTs\fR
same as: <<NO FLAGS>>, but allows some other flags
.HP
\fB\-SCSurface\fR same as: \fB\-drop\fR \fB\-rad1\fR.4         \fB\-out\fR "not water"
.TP
\fB\-EXPOsed\fR
same as: \fB\-drop\fR \fB\-rad1\fR.4         \fB\-out\fR      (note: user supplies pattern)
.TP
\fB\-ASurface\fR
same as: \fB\-drop\fR \fB\-rad0\fR.0 \fB\-add1\fR.4 \fB\-out\fR "not water"
.TP
\fB\-ACCESS\fR
same as: \fB\-drop\fR \fB\-rad0\fR.0 \fB\-add1\fR.4 \fB\-out\fR      (note: user supplies pattern)
.HP
\fB\-SCAN0\fR same as: \fB\-4H\fR \fB\-mc\fR \fB\-self\fR "alta blt40 ogt33"
.HP
\fB\-SCAN1\fR same as: \fB\-4H\fR \fB\-once\fR "sc alta blt40 ogt33" "alta blt40 ogt65,(not water ogt33)"
.TP
\fB\-DUMPAtominfo\fR
count the atoms in the selection: src
.IP
(note that BOTH and ONCE require two patterns while
.IP
OUT, SELF and DUMPATOMINFO require just one pattern)
.TP
\fB\-Implicit\fR
implicit hydrogens
.TP
\fB\-Explicit\fR
explicit hydrogens (default)
.TP
\fB\-DEnsity\fR#
set dot density (default 16 dots/sq A)
.TP
\fB\-Radius\fR#.#
set probe radius (default 0.25 A)
.TP
\fB\-ADDvdw\fR#.#
offset added to Van der Waals radii (default 0.0)
.HP
\fB\-SCALEvdw\fR#.# scale factor for Van der Waals radii (default 1.0)
.TP
\fB\-COSCale\fR#.#
scale C=O carbon Van der Waals radii (default 0.94)
.TP
\fB\-SPike\fR
draw spike instead of dots (default)
.TP
\fB\-SPike\fR#.#
set spike scale (default=0.5)
.TP
\fB\-NOSpike\fR
draw only dots
.HP
\fB\-HBRegular\fR#.# max overlap for regular Hbonds(default=0.6)
.HP
\fB\-HBCharged\fR#.# max overlap for charged Hbonds(default=0.8)
.TP
\fB\-Keep\fR
keep nonselected atoms (default)
.TP
\fB\-DRop\fR
drop nonselected atoms
.TP
\fB\-LIMit\fR
limit bump dots to max dist when kissing (default)
.TP
\fB\-NOLIMit\fR
do not limit bump dots
.TP
\fB\-LENs\fR
add lens keyword to kin file
.TP
\fB\-NOLENs\fR
do not add lens keyword to kin file (default)
.TP
\fB\-MC\fR
include mainchain\->mainchain interactions
.TP
\fB\-HETs\fR
include dots to non\-water HET groups (default)
.TP
\fB\-NOHETs\fR
exclude dots to non\-water HET groups
.TP
\fB\-WATers\fR
include dots to water (default)
.TP
\fB\-NOWATers\fR
exclude dots to water
.TP
\fB\-WAT2wat\fR
show dots between waters
.TP
\fB\-DUMPH2O\fR
include water H? vectorlist in output
.TP
\fB\-4H\fR
extend bond chain dot removal to 4 for H (default)
.TP
\fB\-3\fR
limit bond chain dot removal to 3
.TP
\fB\-2\fR
limit bond chain dot removal to 2
.TP
\fB\-1\fR
limit bond chain dot removal to 1
.HP
\fB\-IGNORE\fR "pattern" explicit drop: ignore atoms selected by pattern
.TP
\fB\-DOCHO\fR
recognize CH..O Hbonds
.TP
\fB\-CHO\fR#.#
scale factor for CH..O Hbond score (default=0.5)
.TP
\fB\-PolarH\fR
use short radii of polar hydrogens (default)
.TP
\fB\-NOPolarH\fR
do not shorten radii of polar hydrogens
.HP
\fB\-NOFACEhbond\fR do not identify HBonds to aromatic faces
.HP
\fB\-Name\fR "name" specify the group name (default "dots")
.TP
\fB\-DOTMASTER\fR
group name used as extra master={name} on lists
.TP
\fB\-NOGroup\fR
do not generate @group statement in .kin format output
.TP
\fB\-KINemage\fR
add @kinemage 1 statement to top of .kin format output
.TP
\fB\-Countdots\fR
produce a count of dots\-not a dotlist
.TP
\fB\-Unformated\fR
output raw dot info
.IP
name:pat:type:srcAtom:targAtom:mingap:gap:spX:
spY:spZ:spikeLen:score:stype:ttype:x:y:z:sBval:tBval:
.TP
\fB\-OFORMAT\fR
output dot info formatted for display in O
.TP
\fB\-XVFORMAT\fR
output dot info formatted for display in XtalView
.TP
\fB\-ONELINE\fR
output one line :contacts:by:severity:type:
.TP
\fB\-GAPcolor\fR
color dots by gap amount (default)
.TP
\fB\-ATOMcolor\fR
color dots by atom type
.TP
\fB\-BASEcolor\fR
color dots by nucleic acid base type
.TP
\fB\-COLORBase\fR
color dots by gap and nucleic acid base type
.HP
\fB\-OUTCOLor\fR "name" specify the point color for \fB\-OUT\fR (default "gray")
.TP
\fB\-GAPWeight\fR#
set weight for scoring gaps (default 0.25)
.HP
\fB\-BUMPWeight\fR# set relative scale for scoring bumps (default 10.0)
.TP
\fB\-HBWeight\fR#
set relative scale for scoring Hbonds (default 4.0)
.TP
\fB\-DIVLow\fR#.#
Division for Bump categories    (default \fB\-0\fR.4)
.TP
\fB\-DIVHigh\fR#.#
Division for Contact categories (default  0.25)
.TP
\fB\-MINOCCupancy\fR#.#
Occupancy below this is same as zero (default  0.02)
.TP
\fB\-ELEMent\fR
add master buttons for different elements in kin output
.TP
\fB\-NOHBOUT\fR
do not output contacts for HBonds
.TP
\fB\-NOCLASHOUT\fR
do not output contacts for clashes
.TP
\fB\-NOVDWOUT\fR
do not output contacts for van der Waals interactions
.TP
\fB\-ONLYBADOUT\fR
onlybadout output bad clashes (severe overlap contacts)
.TP
\fB\-SUMMARY\fR
output summary list of contacts and clashes
.TP
\fB\-ONELINE\fR
output summary list on oneline
.TP
\fB\-NOTICKs\fR
do not display the residue name ticker during processing
.TP
\fB\-STDBONDs\fR
assume only standard bonding patterns in standard residues
.TP
\fB\-NOPARENT\fR
do not bond hydrogens based on table of parent heavy atoms
.TP
\fB\-SEGID\fR
use the PDB SegID field to descriminate between residues
.TP
\fB\-OLDU\fR
generate old style \fB\-u\fR output: kissEdge2BullsEye, etc
.TP
\fB\-VErbose\fR
verbose mode (default)
.TP
\fB\-REFerence\fR
display reference string
.TP
\fB\-CHANGEs\fR
display a list of program changes
.TP
\fB\-Quiet\fR
quiet mode
.TP
\fB\-Help\fR
show expanded help notice (includes other flags)
.TP
\fB\-VERSION\fR
one line version to stdout
.PP
Pattern elements:  (should be put in quotes on the command line)
.TP
FILE#
within file #
.TP
MODEL#
within model #
.TP
CHAINaa
within chain a
.TP
SEGaaaa
segment identifier aaaa (where _ represents blank)
.TP
ALTa
alternate conformation a
.TP
ATOMaaaa
atom name aaaa (where _ represents blank)
(all 4 characters are used so H would be ATOM_H__)
.TP
RESaaa
residue aaa
.TP
#
residue #
.TP
#a
residue #, insert a
.TP
#\-#
residue range # (insert codes ignored)
.TP
a
residue type by one letter codes   (eg. y)
.TP
aaa
residue type by three letter codes (eg. tyr)
.IP
ALL,PROTEIN,MC,SC,BASE,ALPHA,BETA,NITROGEN,CARBON,
OXYGEN,SULFUR,PHOSPHORUS,HYDROGEN,METAL,POLAR,
NONPOLAR,CHARGED,DONOR,ACCEPTOR,AROMATIC,METHYL,
HET,WATER,DNA,RNA
.IP
all or a subset of the atoms
.TP
OLT#
Occupancy less than # (integer percent)
.TP
OGT#
Occupancy greater than # (integer percent)
.TP
BLT#
B\-value less than # (integer)
.TP
BGT#
B\-value greater than # (integer)
.TP
INSa
Insert code a (where _ represents blank)
.TP
WITHIN #.# OF #.#, #.#, #.#
atoms within distance from point
.IP
Patterns can be combined into comma separated lists
such as "trp,phe,tyr" meaning TRP or PHE or TYR.
.IP
Patterns that are sepatated by blanks must all be true
such as "chainb 1\-5" meaning residues 1 to 5 in chain B.
.IP
You can also group patterns with parenthesis, separate
multiple patterns with | meaning 'or' and choose the
complement with NOT as in "not file1" meaning not in file 1.
.IP
An autobondrot file is similar to other PDB input files
but it includes information identifying atoms subject to rotations
and other transformations.
.IP
Example autobondrot file fragment showing Calpha\-Cbeta bond rotation
and a periodic torsion penalty function for this rotation
.TP
ATOM
1  CB  TYR    61      34.219  17.937   4.659  1.00  0.00
.TP
bondrot:chi1:78.7:
0:359:5:33.138:18.517: 5.531:34.219:17.937: 4.659
.IP
cos:\-3:60:3:
ATOM      1 1HB  TYR    61      34.766  18.777   4.206  1.00  0.00
ATOM      1 2HB  TYR    61      34.927  17.409   5.315  1.00  0.00
ATOM      1  CG  TYR    61      33.836  16.989   3.546  1.00  0.00
\&...
.IP
Autobondrot commands use colons to separate values
Transformations: BONDROT:id:currAng:start:end:stepSz:x1:y1:z1:x2:y2:z2
.TP
TRANS:
id:currpos:start:end:stepSz:x1:y1:z1:x2:y2:z2
.TP
NULL
# dummy
.TP
Bias functions:
COS:scale:phaseOffset:frequency
POLY:scale:offset:polynomialDegree
CONST:value
.TP
Branching:
SAVE and RESTORE or "(" and ")"
.IP
(e.g. to rotate each Chi and the methyls for isoleucine the
.IP
sequence is: rotChi1/SAVE/rotChi2/rotCD1/RESTORE/rotCG2)
.IP
Set orientation: GO:angle1:angle2:...
Include files:   @filename
Comments:        # comment text
.PP
probe: version 2.13.110909, Copyright 1996\-2011, J. Michael Word