Provided by: king-probe_2.16.160404+git20180613.a09b012-1_amd64 bug


       king-probe - Evaluate and visualize protein interatomic packing


       Syntax: probe input.pdb >> out.kin

              or: probe [flags] "src pattern" ["target pattern"] pdbfiles... >> out.kin

       -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


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

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

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

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

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

              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)"

              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 hydrogens

              explicit hydrogens (default)

              set dot density (default 16 dots/sq A)

              set probe radius (default 0.25 A)

              offset added to Van der Waals radii (default 0.0)

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

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

       -SPike draw spike instead of dots (default)

              set spike scale (default=0.5)

              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)

              do not limit bump dots

       -LENs  add lens keyword to kin file

              do not add lens keyword to kin file (default)

       -MC    include mainchain->mainchain interactions

       -HETs  include dots to non-water HET groups (default)

              exclude dots to non-water HET groups

              include dots to water (default)

              exclude dots to water

              show dots between waters

              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

              recognize CH..O Hbonds

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

              use short radii of polar hydrogens (default)

              do not shorten radii of polar hydrogens

       -NOFACEhbond do not identify HBonds to aromatic faces

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

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

              do not generate @group statement in .kin format output

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

              produce a count of dots-not a dotlist

              output raw dot info


              output dot info formatted for display in O

              output dot info formatted for display in XtalView

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

              color dots by gap amount (default)

              color dots by atom type

              color dots by nucleic acid base type

              color dots by gap and nucleic acid base type

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

              set weight for scoring gaps (default 0.25)

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

              set relative scale for scoring Hbonds (default 4.0)

              Division for Bump categories    (default -0.4)

              Division for Contact categories (default  0.25)

              Occupancy below this is same as zero (default  0.02)

              add master buttons for different elements in kin output

              do not output contacts for HBonds

              do not output contacts for clashes

              do not output contacts for van der Waals interactions

              onlybadout output bad clashes (severe overlap contacts)

              output summary list of contacts and clashes

              output summary list on oneline

              do not display the residue name ticker during processing

              assume only standard bonding patterns in standard residues

              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 mode (default)

              display reference string

              display a list of program changes

       -Quiet quiet mode

       -Help  show expanded help notice (includes other flags)

              one line version to stdout

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

       FILE#  within file #

       MODEL# within model #

              within chain a

              segment identifier aaaa (where _ represents blank)

       ALTa   alternate conformation a

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

       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 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

              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:

       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

              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