- -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