Syntax

The coordinate statement options are carried out when the END statement is issued. If one wants to carry out several coordinate manipulations, each manipulation has to be initiated separately from the main level of X-PLOR.

COORdinates $<$coordinate-statement$>$ END

is invoked from the main level of X-PLOR. The END statement activates execution of the particular operation.

$<$coordinate-statement$>$:==

COPY

[SELEction=$<$selection$>$] copies main coordinate set into comparison set; XCOMP$:=$X,YCOMP$:=$Y,ZCOMP$:=$Z; B,Q are unaffected (default for selection: (ALL) ).

FIT

{ [SELEction=$<$selection$>$] [MASS=$<$logical$>$]
[LSQ=$<$logical$>$] } rotates (if LSQ is TRUE) and translates all main coordinates to obtain a best fit between the selected main and comparison atoms. Translation superimposes the geometric centers (or the centers of mass if MASS is TRUE) of the two coordinate sets. Rotation occurs with the Kabsch (1976) least-squares fitting algorithm. Mass-weighting is applied if MASS is set to TRUE. Upon successful completion of this operation, the Eulerian angles describing the rotation matrix $R$ are stored in the symbols $THETA1, $THETA2, $THETA3, and the translation vector $T$ is stored in the symbols $X, $Y, $Z. The fitted coordinate set $r'$ is related to original set $r$ by $r'=R*r + T$ (default for selection: (ALL); for MASS: FALSE; for LSQ: TRUE).

FRACtionalize

{ [SELEction=$<$selection$>$]
[A=$<$real$>$] [B=$<$real$>$] [C=$<$real$>$]
[ALPHa=$<$real$>$] [BETA=$<$real$>$] [GAMMa=$<$real$>$] } fractionalizes selected coordinates. The X-PLOR convention keeps the direction of the x-axis (x same direction as a; y is in (a,b) plane) and is the same that is used internally by all X-PLOR routines (default for selected atoms: (ALL); for a, b, c: 1.0; for $\alpha, \beta, \gamma$: 90$^{\circ}$).

INITialize

{ [SELEction=$<$selection$>$] } initializes main coordinate set; i.e., X:=9999.0, Y:=9999.0, Z:=9999.0; B,Q are unaffected (default for selection: (ALL) ).

ORIEnt

{ [SELEction=$<$selection$>$] [MASS=$<$logical$>$]
[LSQ=$<$logical$>$] } rotates (if LSQ is TRUE) and translates all coordinates such that the principal axis system of the selected atoms corresponds to the x,y,z axis. The translation superimposes the geometric center (or the center of mass if MASS is TRUE) and the coordinate origin. The rotation occurs with the Kabsch (1976) least-squares fitting algorithm. Mass-weighting is applied if MASS is set to TRUE. Upon successful completion of this operation, the Eulerian angles describing the rotation matrix $R$ are stored in the symbols $THETA1, $THETA2, $THETA3, and the translation vector $T$ is stored in the symbols $X, $Y, $Z. The oriented coordinate set $r'$ is related to original set $r$ by $r'=R*r + T$ (default for selection: (ALL); for MASS: FALSE; for LSQ: TRUE).

ORTHogonalize

{ [SELEction=$<$selection$>$]
[A=$<$real$>$] [B=$<$real$>$] [C=$<$real$>$]
[ALPHa=$<$real$>$] [BETA=$<$real$>$] [GAMMa=$<$real$>$] } orthogonalizes selected coordinates. The X-PLOR convention keeps the direction of the x-axis (x same direction as a; y is in (a,b) plane) and is the same that is used internally by all X-PLOR routines (default for selected atoms: (ALL); for a, b, c: 1.0; for $\alpha, \beta, \gamma$: 90$^{\circ}$).

RGYRation

{ [SELEction=$<$selection$>$] [MASS=$<$logical$>$]
[FACT=$<$real$>$] } computes radius of gyration

$$R_{gyr}=\sqrt{<{(r_i-<r_i>)}^{2}>}$$ (6.1)

where the angle brackets denote averaging over selected atoms. The averaging is mass-weighted if MASS is TRUE. The factor FACT is subtracted from the masses before applying the mass-weighting. The symbols $RG (radius of gyration), $XCM, $YCM, $ZCM (center of mass) are declared (default for selected atoms: (ALL); for MASS: FALSE; for FACT: 0.0).

RMS

{ [SELEction $<$selection$>$] [MASS=$<$logical$>$] } computes the (mass-weighted if MASS is TRUE) rms difference for selected atoms between the main and comparison set. The rms value is stored in the symbol $RESULT. The individual atomic rms differences are stored in the RMSD array (default for selection: (ALL); for MASS: FALSE).

ROTAte

{ [SELEction=$<$selection$>$] [CENTer=$<$3d-vector$>$]
$<$matrix$>$ } rotates selected atoms around the specified rotation center (default: ( 0 0 0) ). The rotation matrix is specified through the matrix statement (see Section 2.4) (default for selection: (ALL)).

SHAKe

{ [MASS=$<$logical$>$] [REFErence=MAIN$\vert$COMP] } iteratively modifies main coordinate set until SHAKE constraints (see Section 8.2) are satisfied. The reference coordinate set specifies the direction of the SHAKE shift vectors (default for MASS: FALSE; for REFErence: MAIN).

SWAP

{ [SELEction=$<$selection$>$] } exchanges main and comparison coordinate set, i.e., X,Y,Z $\leftrightarrow$ XCOMP,YCOMP,ZCOMP; B,Q are unaffected (default for selection: (ALL) ).

SYMMetry

$<$symmetry-operator$>$ [SELEction=$<$selection$>$] applies the specified crystallographic symmetry operator to the selected coordinates. The notation for the symmetry operator is the same as in the International Tables for Crystallography (Hahn, 1987), e.g., ($-x$, ${y+1}/2$, $-z$). The unit cell geometry needs to be specified (Section 13.3) before invoking this statement. The coordinates are converted into fractional coordinates before application of the symmetry operator and converted back into orthogonal coordinates afterward.

TRANslate

{ [SELEction=$<$selection$>$] VECTor=$<$3d-vector$>$ [DISTance=$<$real$>$] } translates selected atoms by specified translation vector. If DISTance is specified, the translation occurs along the specified vector for the specified distance (default for selection: (ALL) ).

COOR $<$coordinate-read-statement$>$ END

reads coordinates. It is invoked from the main level of X-PLOR.

$<$coordinate-read-statement$>$:==

[DISPosition= COMParison $\vert$
DERIvative $\vert$ MAIN $\vert$ REFErence ] [SELEction=$<$selection$>$]
{ $<$pdb-record$>$ } reads Brookhaven Data Bank formatted records consisting of x,y,z coordinates, occupancies, and B-factors, tries to match the atom name, residue name, residue number, and segment name, and deposits the information in the main (X,Y,Z,B,Q), comparison (XCOMP, YCOMP, ZCOMP, BCOMP, QCOMP), reference (REFX, REFY, REFZ, HARM, HARM), or derivative (DX, DY, DZ, FBETA, FBETA) coordinate arrays. (For the definition of these arrays, see Section 2.16.) The information is deposited only if the atom has been selected. Note that the syntax is strict; i.e., the SELEction and the DISPosition have to be specified before one can read a $<$pdb-record$>$. Also, the PDB convention suggests an END statement at the end of the file that will terminate the coordinate statement (default for selected atoms: (ALL); for DISPosition: MAIN).

$<$pdb-record$>$:==

According to the Brookhaven Protein Data Bank, the entry for atoms is defined as follows:

ATOM    837 HG23 THR  1055      -8.573   5.657  -3.818  1.00  0.00          
ATOM   1223  O   GLY   153A    -11.704  -9.200    .489  1.00  0.80
      uuuuu vvvv uuuuCuuuuI   vvvvvvvvuuuuuuuuvvvvvvvvuuuuuuvvvvvv iii  
        atom     residue          x      y        z     q      b    entry# 
    number name name number     
                          ^ insertion character
                     ^ chain identifier
            ^ additional character for some atom names (mostly h's)

X-PLOR does not use the chain identifier information. Instead, it uses the characters in columns 73-76 for the segment name (see Section 3.7). The segment name has to match the definition in the segment statement. The insertion character is treated as part of the residue number (note: the residue number is a string consisting of a maximum of four characters). X-PLOR ignores any reference to the atom numbers and instead generates its own numbering scheme. The REMARK record of PDB files is treated as a title record (cf. REMARKS, Section 2.8). No other type of PDB specification, such as HETAT, SCALE, or SEQU, is interpreted at present. These additional records have to be removed before one reads PDB coordinates with X-PLOR. Initially, the user should divide the original PDB file into files containing individual protein chains, individual substrates, all waters combined, and individual cofactors. This will simplify the molecular structure generation with X-PLOR (see Section 3.7). Normally, X-PLOR expects orthogonal coordinates. The ORTHogonalize option can be used to convert fractional coordinates into orthogonal Å coordinates (see Section 13.2).

The PDB convention requires an END statement at the end of the coordinate file. X-PLOR uses the same convention. The inclusion of the END statement implies that the coordinate statement must not be terminated with an END statement from the main level of X-PLOR. However, if the END statement is missing in the coordinate file, parsing errors will result.