Syntax:
$ EDPDB [file_name_1 [mark_1]] [file_name_2
[mark_2]] [/EDPINI[=edp_file]]
Note:
1) A mark is a character string which can be used to distinguish
different peptide chains. It is particularly useful when more
than one PDB files are read in and the peptide chains need to
be distinguished. Whenever a new chain is found, its chain
name will be replaced with a new character in the character
string of the mark, unless the character is an underscore `_'. In
the latter case (which is the default), no substitution will be
made. If all of the characters in the string have already been
used, it starts from the first character of the string again. A
string of mark characters of alphabetic order may be
abbreviated with a hyphen, `-'. For example, a-f
is equivalent to abcdef.
2) For the VMS version, the default file type of the input file is
.pdb.
3) The edp_file is the file name of a macro which can be used
to customize the initial configuration of EDPDB. The default
file name is edpini.edp, if the qualifier /EDPINI is specified.
See also: QUIT
Examples:
1) Start EDPDB by reading a PDB file, pdb4lzm.pdb, on a VMS
computer.
$ edpdb pdb4lzm
2) Read two PDB files. One contains A, B, C and D four peptide
chains, and is called abcd_1.pdb. The other contains A, B, C and
D four peptide chains too, and is called abcd_2.pdb.
$ edpdb abcd_1.pdb abcd abcd_2.pdb stuv
In this example, the peptide chains from the second PDB file will
be labelled as S, T, U and V.
3) Customize EDPDB with a macro called vms.edp. (See the example in the ALIAS section).
$ edpdb/edpini=vms.edp
! Try this
initialize
zone all
zone
residue
atom
sort dfres
analyze
read file_a.pdb abcd initialize
; input the first file, keeping the chain names
read file_b.pdb efgh
; input the first file, change the chain names
; to E,F,G and H
2) or start the program by typing
$ edpdb file_a.pdb abcd file_b.pdb efgh
See also:
READ
2) If the result is listed on the terminal with a prompt saying " return for more ... ", the result actually has a copy in a file of the same file-name as the 1st input PDB file and a file type of .scr. To save this file, one has to terminate the program using the QUIT command with the SAVE option.
3) To save other intermediate results, one may either run EDPDB in a batch job mode, or redirect the result to a file (eg. edpdb.log) using the following command.
file log edpdb.log
See also:
FILE
file
initialize
write junk.pdb header
reset
! select the records on which the transformation are applied.
...
rtn file rtn.dat
See also:
RTN
group mola from { main from { chain a }}
group molb from { main from { chain b }}
initialize
load mola
overlay molb rtn.dat
chain a
rtn file rtn.dat
A more general aproach can be done with a macro,
match3d.edp.
See also: ALIGN3D, MATCH3D and OVERLAY.
initialize
rtn file rtn_a.dat save rtn_b.dat
2) Calculate the inverse transformation of a given one, eg. in file
rtn.dat, store it in another file, say inv_rtn.dat.
initialize
rtn file rtn.dat inve inv_rtn.dat
3) Multiply the transformation matrix in the file rtn.dat with the
matrix of symmetry operator #2, store the production in rtn.dat.
initialize
rtn symm 2 0 0 0 mult rtn.dat rtn.dat
See also: RTN
initialize
zone 1 - 164
access
See also:
ACCESS
initialize
group molB from { chain B}
chain A
access molB
; get the SAA of molecule A
; in the presence of molecule B
access
; get the SAA of molecule A
; in the absence of molecule B
See also:
ACCESS
group Natm from { atom N* }
group Oatm from { atom O* }
initialize
load Oatm
distance Natm 0.0 3.5 2
See also:
NAYB,
NAYBR,
MMIG and
AB
dfabc ca cb cg 0 0 0 initialize atom ca cb cg abc2) Calculate the angle that formed by atoms from different residues, eg. the C-O-OH angle, where C and O are the carbonyl carbon and the carbonyl oxygen atoms of an amino acid residue and OH is a water molecule.
dfbrg C O OH CA x 0 x 0 ,,,, 0.0 3.5 0.0 180.0 0.0 360.0 zwxy ; The 1st 'x 0' indicates that the C atom (atom_w) belongs ; to the same residue as the O atom (atom_x). ; The 2nd 'x 0' indicates that the CA atom (atom_z) also ; belongs to the same residue as the O atom (atom_x). ; The O-OH distance, the C-O-OH angle and CA-C-O-OH torsion ; angle will be calculated. initialize atom C O OH bridgeSee also: ABC and BRIDGE
@phipsi
write phipsi.lis
2) Calculate the chi (I,II) angles.
@chi
write chi.lis
3) Calculate the zeta angles to check chirality.
initialize
dfabcd ca n c cb
atom ca n c cb
abcd
quit save
See also:
ABCD command and
RTN ABCD command.
dfbrg cb sg sg cb x 0 y 0
residue cys
2) Search for candidates of sites of engineered disulfide bridges.
The search criterion is the following. The two residues should be
20 residues apart in the amino acid sequence. The Cb-Cb distance
should be between 2.5 and 6.0 Å. One of the Ca-Cb-Cb angle
should be between 80.0 and 180.0 degrees. (The Ca-Cb-Cb-Ca
torsional angle is unrestricted).
initialize
dfbrg ca cb cb ca x 0 y 0 t t t t 2.5 6.0 80 180 0 360 wxyz 20
atom ca cb
bridge
initialize
group n_a from { main a15 - a60 }
group n_b from { main b15 - b60 }
load n_a
overlay n_b match_n_domain.dat
initialize
group c_a from { main a80 - a160 }
group c_b from { main b80 - b160 }
load c_a
rtn file match_n_domain.dat
overlay c_b match_c_domain.dat
initialize
axis match_c_domain.dat
; the hinge bending angle will be listed
; with the AXIS command.
! for each protein molecule you may create
! a PDB file containing the protein and the associated solvents
! using a macro similar to the following
cell 100 100 100 90 90 90 1
! ^^^^ your cell parameters
! the last number is important if your cell is not
! orthogonal.
@p212121
!^^^ your space group
initialize
zone a1 - a234
! ^^^^^^^^^ your protein zone
system rm tmpa.pdb
write tmpa.pdb
! ^^^^ your new pdb file name
group prta
initialize
{atom O2H | residue SOL}
! ^^^ your solvent atom name(s)
mmig prta 4.0 move_all
! ^^^ cutoff for a solvent molecule to be considered
! associated with one protein molecule
quit
! % edpdb tmpa.pdb a tmpb.pdb b
! ^ ^
! define molecules a and b
! superimpose the two protein molecules using CA atoms
initialize
{ ca | zone a1 - a234 } ; select CA atoms from chain a
! ^^^ your protine zone
group prta
initialize
{ ca | zone b1 - b234 } ; select CA atoms from chain b
! ^^^ your protein zone
over prta b_to_a.dat
! ^^^^ matrix from molecule b to a
initialize
chain b
rtn file b_to_a.dat
! apply the matrix to molecule b including its solvent molecules
initialize
{ atom O2H | residue SOL | chain b }
! ^^^ your solvent atom name
group solb
initialize
{ atom O2H | residue SOL | chain a }
! ^^^ your solvent atom name
distance solb 0 1.2 0 1000
! ^^^ your choice for two solvent molecules to be related.
quit save
! check the tmpa.scr file
1) Reset the entry number
sete
2) Split the chain name from the residue number in the input
residue id.
seti
See also: the editing category.
zone all
sort B
list
2) Sort the records according to X coordinates
zone all
setw x
sort w
list
See also:
SORT and
SETW
initialize
cell 61.2 61.2 96.8 90 90 120 1
symmetry x, +y, +z
symmetry -y, x-y, +z+2/3
symmetry -x+y, -x, +z+1/3
symmetry +y, x, -z
symmetry -x, -x+y, -z+2/3
symmetry x-y, -y, -z+1/3
2) Check the crystal packing contacts between molecules A and B.
group mola from { chain A }
group molb from { chain B }
initialize
load mola
mmig mola 4.0 ; check A-A contacts
mmig molb 4.0 ; check A-B contacts
initialize
load molb
mmig molb 4.0 ; check B-B contacts
3) The solution of a molecular replacement search may put the
protein molecule in an asymmetric unit which is far away from the
origin. The MOVECENTER command can bring the molecule
close to the origin (or any user specified asymmetric unit).
zone all
movecenter rtn.dat 0.0 0.0 0.0 0.5 0.5 0.5
rtn file rtn.dat
See also:
SYMMETRY,
MMIG and
MOVECENTER
! First, input the polar angles using a PDB format file cell 61.2 61.2 96.8 90.0 90.0 120.0 1 ; input the cell parameters @p3221 ; input the symmetry operators using a macro file zone all list ; take a look of the initial peaks polar to_polar ; standardize the angles list ; take a look again polar asymm ; convert the peaks to one asymmetric unit list polar unique 3. ; exclude redandent peaks list reset zone all polar move_to_o 1 ca ; apply a rotation such that the first peak, ; which is stored in the "CA" record of the residue "1", ; will move to the origin. list2) Assume that the space group is P3(2)21; the positions of the self rotation function solution peaks are stored in a PDB format file.
! First, input the polar angles using a PDB format file cell 61.2 61.2 96.8 90.0 90.0 120.0 1 ; input the cell parameters @p3221 ; input the symmetry operators using a macro file zone all list ; take a look of the initial peaks polar srf_red ; convert the peaks to one asymmetric unit list polar unique 3. ; exclude redandent peaks list
initialize
zone all
write backup.pdb ; save the current file for safety
@mutate 6 ile ; a VMS version macro
; to run this macro, one may need to copy the aalib.pdb
; to the current directory.
2) Set the chi-I and chi-II angles of residue 6 Ile to -60 and 170
degrees using a macro file, set_chi_ile.edp.
@set_chi_ile 6 -60 170
where set_chi_ile.edp contains the following.
! set_chi_ile.edp
initialize
side $(p1)
rtn abcd $(p1) n $(p1) ca $(p1) cb $(p1) cg1 $(p2)
exclude atom cg2
rtn abcd $(p1) ca $(p1) cb $(p1) cg1 $(p1) cd1 $(p3)
or simply
@set_chi 6 -60 170
1) Change the Ca position of residue 164.
initialize
ca 164
rtn overlay 164 N C CB 0 0 0 , ,,, ,,, inve tmp.dat
rtn matrix -1 0 0 0 1 0 0 0 1 0 0 0
rtn file tmp.dat
See also: the macros fix_hand.edp.
2) Change the position of the side chain of residue 164.
initialize
side 164
rtn overlay 164 N CA C 0 0 0 , ,,, ,,, inve tmp.dat
rtn matrix -1 0 0 0 1 0 0 0 1 0 0 0
rtn file tmp.dat
1) To build a molecule from scratch, See also: the examples in the NEWXYZ section
2) To build a molecule from pieces of fragments, see RTN OVERLAY command.
zone all
polar to_euler