Flags:¶

-SElf

self intersection: src -> src (default)

-Both

intersect both ways: src <=> targ

-ONce

single intersection: src -> targ

-OUt

external van der Waals surface of src (solvent contact surface)

-AUTObondrot filename

read and process an autobondrot file

shortcuts:

<<NO FLAGS>>same as: -4H -mc -het -self "altA ogt33"

-DEFAULTs

same as: <<NO FLAGS>>, but allows some other flags

-SCSurface same as: -drop -rad1.4 -out "not water"

-EXPOsed

same as: -drop -rad1.4 -out (note: user supplies pattern)

-ASurface

same as: -drop -rad0.0 -add1.4 -out "not water"

-ACCESS

same as: -drop -rad0.0 -add1.4 -out (note: user supplies pattern)

-SCAN0 same as: -4H -mc -self "alta blt40 ogt33"

-SCAN1 same as: -4H -once "sc alta blt40 ogt33" "alta blt40 ogt65,(not water ogt33)"

-DUMPAtominfo

count the atoms in the selection: src

(note that BOTH and ONCE require two patterns while

OUT, SELF and DUMPATOMINFO require just one pattern)

-Implicit

implicit hydrogens

-Explicit

explicit hydrogens (default)

-DEnsity#

set dot density (default 16 dots/sq A)

-Radius#.#

set probe radius (default 0.25 A)

-ADDvdw#.#

offset added to Van der Waals radii (default 0.0)

-SCALEvdw#.# scale factor for Van der Waals radii (default 1.0)

-COSCale#.#

scale C=O carbon Van der Waals radii (default 0.94)

-SPike

draw spike instead of dots (default)

-SPike#.#

set spike scale (default=0.5)

-NOSpike

draw only dots

-HBRegular#.# max overlap for regular Hbonds(default=0.6)

-HBCharged#.# max overlap for charged Hbonds(default=0.8)

-Keep

keep nonselected atoms (default)

-DRop

drop nonselected atoms

-LIMit

limit bump dots to max dist when kissing (default)

-NOLIMit

do not limit bump dots

-LENs

add lens keyword to kin file

-NOLENs

do not add lens keyword to kin file (default)

-MC

include mainchain->mainchain interactions

-HETs

include dots to non-water HET groups (default)

-NOHETs

exclude dots to non-water HET groups

-WATers

include dots to water (default)

-NOWATers

exclude dots to water

-WAT2wat

show dots between waters

-DUMPH2O

include water H? vectorlist in output

-4H

extend bond chain dot removal to 4 for H (default)

-3

limit bond chain dot removal to 3

-2

limit bond chain dot removal to 2

-1

limit bond chain dot removal to 1

-IGNORE "pattern" explicit drop: ignore atoms selected by pattern

-DOCHO

recognize CH..O Hbonds

-CHO#.#

scale factor for CH..O Hbond score (default=0.5)

-PolarH

use short radii of polar hydrogens (default)

-NOPolarH

do not shorten radii of polar hydrogens

-NOFACEhbond do not identify HBonds to aromatic faces

-Name "name" specify the group name (default "dots")

-DOTMASTER

group name used as extra master={name} on lists

-NOGroup

do not generate @group statement in .kin format output

-KINemage

add @kinemage 1 statement to top of .kin format output

-Countdots

produce a count of dots-not a dotlist

-Unformated

output raw dot info

name:pat:type:srcAtom:targAtom:mingap:gap:spX: spY:spZ:spikeLen:score:stype:ttype:x:y:z:sBval:tBval:

-OFORMAT

output dot info formatted for display in O

-XVFORMAT

output dot info formatted for display in XtalView

-ONELINE

output one line :contacts:by:severity:type:

-GAPcolor

color dots by gap amount (default)

-ATOMcolor

color dots by atom type

-BASEcolor

color dots by nucleic acid base type

-COLORBase

color dots by gap and nucleic acid base type

-OUTCOLor "name" specify the point color for -OUT (default "gray")

-GAPWeight#

set weight for scoring gaps (default 0.25)

-BUMPWeight# set relative scale for scoring bumps (default 10.0)

-HBWeight#

set relative scale for scoring Hbonds (default 4.0)

-DIVLow#.#

Division for Bump categories (default -0.4)

-DIVHigh#.#

Division for Contact categories (default 0.25)

-MINOCCupancy#.#

Occupancy below this is same as zero (default 0.02)

-ELEMent

add master buttons for different elements in kin output

-NOHBOUT

do not output contacts for HBonds

-NOCLASHOUT

do not output contacts for clashes

-NOVDWOUT

do not output contacts for van der Waals interactions

-ONLYBADOUT

onlybadout output bad clashes (severe overlap contacts)

-SUMMARY

output summary list of contacts and clashes

-ONELINE

output summary list on oneline

-NOTICKs

do not display the residue name ticker during processing

-STDBONDs

assume only standard bonding patterns in standard residues

-NOPARENT

do not bond hydrogens based on table of parent heavy atoms

-SEGID

use the PDB SegID field to descriminate between residues

-OLDU

generate old style -u output: kissEdge2BullsEye, etc

-VErbose

verbose mode (default)

-REFerence

display reference string

-CHANGEs

display a list of program changes

-Quiet

quiet mode

-Help

show expanded help notice (includes other flags)

-VERSION

one line version to stdout

Pattern elements: (should be put in quotes on the command line)

FILE#

within file #

MODEL#

within model #

CHAINaa

within chain a

SEGaaaa

segment identifier aaaa (where _ represents blank)

ALTa

alternate conformation a

ATOMaaaa

atom name aaaa (where _ represents blank) (all 4 characters are used so H would be ATOM_H__)

RESaaa

residue aaa

#

residue #

#a

residue #, insert a

#-#

residue range # (insert codes ignored)

a

residue type by one letter codes (eg. y)

aaa

residue type by three letter codes (eg. tyr)

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

all or a subset of the atoms

OLT#

Occupancy less than # (integer percent)

OGT#

Occupancy greater than # (integer percent)

BLT#

B-value less than # (integer)

BGT#

B-value greater than # (integer)

INSa

Insert code a (where _ represents blank)

WITHIN #.# OF #.#, #.#, #.#

atoms within distance from point

Patterns can be combined into comma separated lists such as "trp,phe,tyr" meaning TRP or PHE or TYR.

Patterns that are sepatated by blanks must all be true such as "chainb 1-5" meaning residues 1 to 5 in chain B.

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.

An autobondrot file is similar to other PDB input files but it includes information identifying atoms subject to rotations and other transformations.

Example autobondrot file fragment showing Calpha-Cbeta bond rotation and a periodic torsion penalty function for this rotation

ATOM

1 CB TYR 61 34.219 17.937 4.659 1.00 0.00

bondrot:chi1:78.7:

0:359:5:33.138:18.517: 5.531:34.219:17.937: 4.659

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 ...

Autobondrot commands use colons to separate values Transformations: BONDROT:id:currAng:start:end:stepSz:x1:y1:z1:x2:y2:z2

TRANS:

id:currpos:start:end:stepSz:x1:y1:z1:x2:y2:z2

NULL

# dummy

Bias functions:

COS:scale:phaseOffset:frequency POLY:scale:offset:polynomialDegree CONST:value

Branching:

SAVE and RESTORE or "(" and ")"

(e.g. to rotate each Chi and the methyls for isoleucine the

sequence is: rotChi1/SAVE/rotChi2/rotCD1/RESTORE/rotCG2)

Set orientation: GO:angle1:angle2:... Include files: @filename Comments: # comment text

probe: version 2.13.110909, Copyright 1996-2011, J. Michael Word