Program : XPAND
Version : 050427
Author : Gerard J. Kleywegt, Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 596,
SE-751 24 Uppsala, SWEDEN
E-mail : gerard@xray.bmc.uu.se
Purpose : symmetry and NCS expansion of molecules
Package : X-UTIL
Reference(s) for this program:
* 1 * G.J. Kleywegt (1992-2004). Uppsala University, Uppsala, Sweden. Unpublished program.
* 2 * Kleywegt, G.J., Zou, J.Y., Kjeldgaard, M. & Jones, T.A. (2001). Around O. In: "International Tables for Crystallography, Vol. F. Crystallography of Biological Macromolecules" (Rossmann, M.G. & Arnold, E., Editors). Chapter 17.1, pp. 353-356, 366-367. Dordrecht: Kluwer Academic Publishers, The Netherlands.
940512 - 0.1 - first version
940513 - 0.2 - a bit more
941219 - 0.3 - added X-PLOR (X)NCS option
950109 - 0.4 - started BONDAGE option
950130 - 0.5 - remove all duplicate operators in X option
950220 - 0.6 - added Water scrutinizer option
951022 - 0.7 - made sensitive to OSYM
951030 - 1.0 - added command to generate PDB MTRIX cards;
enable reading of one OR MANY NCS operators
from each file for options N, M, B, and X
951127 - 1.1 - changed Water command such that the output can be
written to a log file and (optionally) the waters
which look okay can be written to a new PDB file
980311 - 1.2 - print error message if something goes wrong
980901 - 1.3 - added Invert command to invert O-style Cartesian
space RT operators
981124 -1.3.1- minor bug fix (if all atoms have identical
coordinates, the program used to crash)
010628 - 1.4 - added C option to generate CNS (X)NCS blurb for
"ncs.def" file
010905 -1.4.1- bug fix in C option (format was wrong and limited
the nr of nb_ncs_matrix_* to 9)
020208 -1.4.2- bug fix in B option (nothing serious, but crashed
on Linux)
020308 -1.4.3- increased max nr of NCS operators to 180, and max nr
of atoms to 100000
020309 -1.4.4- option to auto-generate chain IDs in mode 'N' (handy
if you have 180-fold NCS ...)
031223 - 1.5 - new command "A" to expand under SGS around a point
040224 -1.5.1- minor bug fix (for Alpha version)
040318 -1.5.2- minor changes
040917 - 1.6 - added a new option to command "F" that enables the user
to either do fractional expansion of the molecule as a
whole, or of each atom individually;
new command "D" to extract the default cell constants
and spacegroup name from a PDB file (saves you some
typing
041001 - 1.7 - replaced Kabsch' routine U3BEST by quaternion-based
routine (U3QION) to do least-squares superpositioning
050331 -1.7.1- modified the "F" command; it now first asks if you
want to expand the Molecule or the individual Atoms.
If you select Atoms, the allowed fractional expansion
range now runs from -1 to +2 in all three directions !
050425 -1.7.2- fixed a nasty bug in the "F" command (thanks to Charlie
Bond for pointing out the problem)
050427 - 1.8 - new commands O and R to convert PDB-style MTRIX and
"REMARK 350 BIOMT" operators to O format
XPAND is a simple little program that can be used in conjunction with the SYMMETRY commands in O. The output PDB files can be used for investigating crystal contacts, packing etc.
At present, the following options exist:
- N = expand a PDB file under NCS;
instead of doing lots of "sam_at_in" and "lsq_mol"
inside O, you can use this option to apply each
of your NCS operators to your structure. The output
is a PDB file containing all NCS-related molecules.
- E = expand into a sphere under SGS;
this generates all symmetry-related atoms whose distance
to the centre-of-gravity of your molecule is less than
(RADMAX + MARGIN), where RADMAX is the maximum distance
of any atom inside your structure to the centre-of-gravity,
and MARGIN is a number you provide (e.g., 5 A). The output
is a PDB file containing all these atoms. This option
is a useful substitute for the "SYMM_SPHERE" command in O,
since you now get one PDB file (and, therefore, one
molecule in O, and only one graphics object) containing
all nearby symmetry-related atoms.
NOTE: if multiple copies of a residue exist within this
symmetry object you can NOT use the second (or later)
instances for centering or getting distances; however,
you WILL be able to identify them (and that's what's
usually the most important).
- P = expand PDB file under SGS;
simply apply each and every one of your spacegroup's
symmetry operators to your structure (not very useful).
- F = expand fractional under SGS;
generate all molecules which have their centre-of-gravity
inside the unit cell [0,+1> (or a smaller part of it).
This can be used to look at packing, for example. In that
case, you may only want to use the CA atoms; use something
like: "grep ATOM m9abcd.pdb | grep CA > cas.pdb" to
extract the CA atom cards.
As of version 1.6, you can also apply this operation to
all the atoms individually, e.g. to fill a unit cell or
asymmetric unit with atoms (whose connectivity may be
screwed up in O, and some of which may have duplicate
names - the user beware !)
- A = expand around a point under SGS;
apply each and every one of your spacegroup's
symmetry operators to your structure, but translate by
an integer number of unit cells along a/b/c so as to
bring the centre-of-gravity of the transformed molecules
as close a spossible to a certain point (defined by
fractional or cartesian coordinates).
- X = generate complete X-PLOR (X)NCS file;
generates all XNCS *AND* NCS relations required for proper
evaluation of crystal contacts in case strict NCS is used
in X-PLOR. Supply all NCS operators, the SGS operators,
the cell constants and a margin (1-10 A).
The program loops over all NCS-related molecules, and for
generates all NCS & SGS related molecules whose centre-of-
gravity is nearby. Each such molecule gives an NCS relation
for the X-PLOR include file. The program filters out:
- operators which are identical to an XNCS operator, &
- operators which are identical to the *inverse* of a
previously generated XNCS or NCS operator.
See also chapter 20.2 of the X-PLOR manual.
NOTE: I *think*, but am *not sure*, that the algorithm works
correctly. Send bug reports to "gerard@xray.bmc.uu.se".
- C = generate CNS (X)NCS blurb for "ncs.def" file;
very similar to option X, except that the output file
needs to be inserted into the example ncs.def file of CNS
- B = bondage;
generate a list of all short contacts between atoms which
are close in space due to NCS and/or SGS. Supply all NCS
operators, the SGS operators, the cell constants and a cut-off
distance for the contacts (e.g., 2.4 A for too close contacts,
3.6 A for salt links and potential hydrogen bonds, or ~4.5-5 A
to include hydrophobic interactions).
- W = water scrutinizer;
checks neighbours of all waters and assesses if waters could
be something else (~iso-electronic) such as NH4+, F-, Na+
or Mg++.
- M = generate PDB MTRIX cards;
generates NCS MTRIX cards for PDB files from a set of O-style
NCS-operators.
- O = convert PDB MTRIX records to O-style RT operator(s);
read a PDB file, extract any and all RT operators from PDB MTRIX
records, and save them to an O-style operator file
- R = convert PDB REMARK 350 records to O-style RT operator(s);
read a PDB file, extract any and all RT operators from PDB
"REMARK 350 BIOMT" records, and save them to an O-style
operator file. This option, followed by "N" can be used
to generate relevant biomolecules (e.g., entire virus
particles) from a PDB file
- I = invert O-style RT operator(s);
read O-style Cartesian space RT-operators (e.g., NCS) from
one or more files, invert the operators, and write them to
a new file
- D = get Default unit cell and spacegroup from PDB file;
to prevent you from having to type the cell constants and spacegroup
name you can extract their default values from a PDB file with
this command. When you are subsequently asked by another
command to supply these items, you can simply hit RETURN.
Of course, this only works if your PDB file contains a
proper CRYST1 card
NOTE: this program is sensitive to the environment variable OSYM.
It should point to your local copy of $ODAT/symm, the directory
which contains the spacegroup symmetry operators in O format.
When asked for a file with spacegroup operators in O format,
you may either provide a filename, or the name of a sapcegroup
(including blanks if you like, case doesn't matter). The program
will try to open the following files, assuming that STRING is the
what you input:
(1) open a file called STRING
(2) if this fails, check if OSYM is defined and open $OSYM/STRING
(3) if this fails, open $OSYM/string.sym
(4) if this fails, open $OSYM/string.o
Hint: if you make soft links in the OSYM directory, you can also type
spacegroup numbers (e.g.: \ln -s p212121.sym 19.sym).
NOTE: from version 0.8 onwards, you may choose to enter NCS operators either one by one (as it used to be), or all in one go (by putting them all in one file), or a mixture of this. The following options are affected: B, M, N, I, and X.
When you start the program, you'll see something like this:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- % 106 gerard sarek 15:53:18 xpand/test > ../6d/6D_XPAND*** XPAND *** XPAND *** XPAND *** XPAND *** XPAND *** XPAND *** XPAND ***
Version - 050427/1.8 (c) 1992-2005 Gerard J. Kleywegt, Dept. Cell Mol. Biol., Uppsala (SE) User I/O - routines courtesy of Rolf Boelens, Univ. of Utrecht (NL) Others - T.A. Jones, G. Bricogne, Rams, W.A. Hendrickson Others - W. Kabsch, CCP4, PROTEIN, E. Dodson, etc. etc.
Started - Wed Apr 27 17:47:46 2005 User - gerard Mode - interactive Host - sarek (Irix/SGI) ProcID - 18794 Tty - /dev/ttyq12
*** XPAND *** XPAND *** XPAND *** XPAND *** XPAND *** XPAND *** XPAND ***
Reference(s) for this program:
* 1 * G.J. Kleywegt (1992-2005). Uppsala University, Uppsala, Sweden. Unpublished program.
* 2 * Kleywegt, G.J., Zou, J.Y., Kjeldgaard, M. & Jones, T.A. (2001). Around O. In: "International Tables for Crystallography, Vol. F. Crystallography of Biological Macromolecules" (Rossmann, M.G. & Arnold, E., Editors). Chapter 17.1, pp. 353-356, 366-367. Dordrecht: Kluwer Academic Publishers, The Netherlands.
==> For manuals and up-to-date references, visit: ==> http://xray.bmc.uu.se/usf ==> For reprints, visit: ==> http://xray.bmc.uu.se/gerard ==> For downloading up-to-date versions, visit: ==> ftp://xray.bmc.uu.se/pub/gerard
*** XPAND *** XPAND *** XPAND *** XPAND *** XPAND *** XPAND *** XPAND ***
Max nr of input atoms = ( 100000) Max nr of SGS operators = ( 96) Max nr of NCS operators = ( 360)
==> SGS = Space Group Symmetry ==> NCS = Non-Crystallographic Symmetry
N = expand PDB file under NCS E = expand into a sphere under SGS P = expand PDB file under SGS F = expand fractional under SGS A = expand around a point under SGS X = generate complete X-PLOR (X)NCS file C = generate CNS (X)NCS blurb for "ncs.def" file B = generate non-bonded contacts (NCS+SGS) W = water scrutinizer M = generate PDB MTRIX records O = convert PDB MTRIX records to O-style RT operator(s) R = convert PDB REMARK 350 records to O-style RT operator(s) I = invert O-style RT operator(s) D = get default unit cell and spacegroup from PDB file ? = print this list of options Q = quit
Task ? (N) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (N) ncs Input PDB file ? (in.pdb) m9a.pdb Output PDB file ? (out.pdb) q.pdbEnter the names of all NCS operator files including the unit operator; finish with <CR>
NCS operator file 1 ? ( ) m9a_to_a.o Opening O datablock : (m9a_to_a.o) Datablock : (.LSQ_RT_M9A_TO_A) Data type : (R) Number : (12) Format : ((3F15.7)) Chain ID for this operator ? (A)
...
NCS operator file 5 ? ( )
Nr of NCS operators : 4 NCSOP 1 = 1.0000000 0.0000000 0.0000000 0.000 0.0000000 1.0000000 0.0000000 0.000 0.0000000 0.0000000 1.0000000 0.000 Determinant of rotation matrix = 1.000000 Rotation angle = 0.000000 NCSOP 2 = -0.9551680 0.2573400 -0.1463910 167.543 0.2482270 0.4265990 -0.8697110 -4.093 -0.1613620 -0.8670580 -0.4713520 41.981 Determinant of rotation matrix = 1.000000 Rotation angle = 179.490646 NCSOP 3 = -0.9942670 -0.0465330 -0.0962680 176.737 -0.0654140 -0.4474780 0.8918990 27.418 -0.0845800 0.8930830 0.4418690 -5.859 Determinant of rotation matrix = 0.999999 Rotation angle = 179.362045 NCSOP 4 = 0.9474510 -0.2256360 0.2267720 7.428 -0.2222160 -0.9741420 -0.0408460 58.262 0.2301240 -0.0116930 -0.9730910 -5.618 Determinant of rotation matrix = 1.000001 Rotation angle = 179.154190
Reading PDB file ...
Nr of lines read : ( 1296) Nr of atoms read : ( 1281)
NCS expansion for operator : ( 1) NCS expansion for operator : ( 2) NCS expansion for operator : ( 3) NCS expansion for operator : ( 4)
Nr of atoms generated : ( 5124) Nr of lines written : ( 5167) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (N) e Input PDB file ? (in.pdb) m9abcd.pdb Output PDB file ? (out.pdb) q.pdb SGS operator file ? (p1.sym) p212121.o Opening O datablock : (p212121.o) Datablock : (A_SYMMOP) Data type : (R) Number : (48) Format : ((3F10.4)) Nr of SGS operators : ( 4)Nr of spacegroup symmetry operators : 4 SYMOP 1 = 1.0000 0.0000 0.0000 0.000 0.0000 1.0000 0.0000 0.000 0.0000 0.0000 1.0000 0.000
...
Cell constants ? ( 100.000 100.000 100.000 90.000 90.000 90.000) 106.820 62.340 114.190 90.00 90.00 90.00 Shell radius (A) ? ( 5.000) 4
Reading PDB file ...
Nr of lines read : ( 5167) Nr of atoms read : ( 5124)
Min XYZ : ( 54.235 -15.476 -30.211) Max XYZ : ( 118.858 51.801 40.164) Centre : ( 87.727 19.607 7.399) Fractl : ( 0.821 0.315 0.065) Farthest atom : ( 4888 OD1 ASP D 133 65.325 17.120 -28.506) Distance : ( 42.394) Max centre distance : ( 88.787)
...
Checking operator : ( 4)
Translation -1 0 0 Distance : ( 56.003) Nr of atoms found : ( 1098)
Translation -1 1 0 Distance : ( 77.587) Nr of atoms found : ( 38)
Translation 0 0 0 Distance : ( 56.003) Nr of atoms found : ( 1155)
Translation 0 1 0 Distance : ( 77.587) Nr of atoms found : ( 0)
Nr of atoms written : ( 4553) Nr of lines written : ( 4651) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (E) p Input PDB file ? (m9abcd.pdb) cas.pdb Output PDB file ? (q.pdb) qq.pdb SGS operator file ? (p212121.o) Opening O datablock : (p212121.o) Datablock : (A_SYMMOP) Data type : (R) Number : (48) Format : ((3F10.4)) Nr of SGS operators : ( 4)Nr of spacegroup symmetry operators : 4 SYMOP 1 = 1.0000 0.0000 0.0000 0.000 0.0000 1.0000 0.0000 0.000 0.0000 0.0000 1.0000 0.000 Determinant of rotation matrix = 1.000000 Rotation angle = 0.000000
...
Cell constants ? ( 106.820 62.340 114.190 90.000 90.000 90.000)
Reading PDB file ...
Nr of lines read : ( 648) Nr of atoms read : ( 632)
Generating operator : ( 2)
Generating operator : ( 3)
Generating operator : ( 4)
Nr of atoms written : ( 2528) Nr of lines written : ( 2554) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Here you can choose to expand a Molecule (which means its centre of gravity is used to decide which symmetry-related copies are to be generated), or all Atoms individually. In the former case, the allowed fractional expansion range is [0,+1> in all three directions. If you expand all atoms, however, the allowed range is [-1,+2>. You could use this, for instance, to generate slightly more than an asymmetric unit or unit cell of atoms and use the output file to generate a solvent-flattening mask with MAMA.
In this example we take a set of peaks and map them into an asymmetric unit of spacegroup P21212:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (F) Fractional Input PDB file ? (iod.pdb) sortedpeaks.pdb Output PDB file ? (out.pdb) out.pdb SGS operator file ? (/home/gerard/oinfo/symm/p21212.sym) p21212 OSYM : (/home/gerard/oinfo/symm/) Opened file : (/home/gerard/oinfo/symm/p21212.sym) Opening O datablock : (/home/gerard/oinfo/symm/p21212.sym) O-style symm-ops for spacegroup P21212 18 4 4 P21212 PG222 ORTHORHOMBIC 'P 21 21 2' Datablock : (.SPACE_GROUP_OPERATORS) Data type : (R) Number : (48) Format : ((3F15.6)) Nr of SGS operators : ( 4)Nr of spacegroup symmetry operators : 4
[...]
Determinant of rotation matrix = 1.000000 Rotation angle = 180.000000 Cell constants ? ( 164.577 110.980 56.295 90.000 90.000 90.000) 164.577 110.98 56.295 90 90 90 Max allowed fractional range [0,+1> Fractional lower limits ? ( 0.000 0.000 0.000) 0.5 0.5 0 Fractional upper limits ? ( 1.000 1.000 1.000) 1 1 1 Select option: M = apply to the Molecule as a whole A = apply to each Atom individually Option (M/A) ? (M) atoms
Reading PDB file ...
Nr of lines read : ( 52) Nr of atoms read : ( 52)
Nr of atoms written : ( 52) Nr of lines written : ( 53)
Off-spring counts : Nr of atoms with 1 off-spring = 52 Nr of atoms with 0 off-spring = 0 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
And here we expand into slightly more than an asymmetric unit in P212121:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (D) f Input PDB file ? (1pmp.pdb) Output PDB file ? (out.pdb) asu.pdb SGS operator file ? (p212121.sym) OSYM : (/home/gerard/oinfo/symm/) Opened file : (/home/gerard/oinfo/symm/p212121.sym) Opening O datablock : (/home/gerard/oinfo/symm/p212121.sym) O-style symm-ops for spacegroup P212121 19 4 4 P212121 PG222 ORTHORHOMBIC 'P 21 21 21' Datablock : (.SPACE_GROUP_OPERATORS) Data type : (R) Number : (48) Format : ((3F15.6)) Nr of SGS operators : ( 4)Nr of spacegroup symmetry operators : 4
[...]
Cell constants ? ( 91.800 99.500 56.500 90.000 90.000 90.000) Select option: M = apply to the Molecule as a whole A = apply to each Atom individually Option (M/A) ? (M) a Max allowed fractional range [-1,+2> Fractional lower limits ? ( 0.000 0.000 0.000) -0.1 -0.1 -0.1 Fractional upper limits ? ( 1.000 1.000 1.000) 1.1 1.1 0.35
Reading PDB file ...
Nr of lines read : ( 3440) Nr of atoms read : ( 3192)
Nr of atoms written : ( 8367) Nr of lines written : ( 8615)
Off-spring counts : Nr of atoms with 6 off-spring = 59 Nr of atoms with 5 off-spring = 87 Nr of atoms with 4 off-spring = 375 Nr of atoms with 3 off-spring = 1084 Nr of atoms with 2 off-spring = 1239 Nr of atoms with 1 off-spring = 348 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
To define the point in terms of fractional coordinates, enter the fractional coordinates and, when prompted for the Cartesian oness, simply hit RETURN. To define the point in terms of Cartesian coordinates, hit RETURN when asked for the fractional coordinates and enter the desired coordinates when asked for the Cartesian ones.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (N) a Input PDB file ? (in.pdb) 1cbq.pdb Output PDB file ? (out.pdb) test.pdb SGS operator file ? (p1.sym) p213.o Opened file : (p213.o) Opening O datablock : (p213.o) Datablock : (.SPACE_GROUP_OPERATORS) Data type : (R) Number : (144) Format : ((3F10.5)) Nr of SGS operators : ( 12)Nr of spacegroup symmetry operators : 12
SYMOP 1 = 1.0000 0.0000 0.0000 0.000 0.0000 1.0000 0.0000 0.000 0.0000 0.0000 1.0000 0.000 Determinant of rotation matrix = 1.000000 Rotation angle = 0.000000
[...]
SYMOP 12 = 0.0000 0.0000 -1.0000 0.500 -1.0000 0.0000 0.0000 0.000 0.0000 1.0000 0.0000 0.500 Determinant of rotation matrix = 1.000000 Rotation angle = 120.000000 Cell constants ? ( 100.000 100.000 100.000 90.000 90.000 90.000) 81.04 81.04 81.04 Fractional point to expand around ? ( 0.000 0.000 0.000) 0 0 0 Cartesian point to expand around ? ( 0.000 0.000 0.000) Fractional : ( 0.000 0.000 0.000) Cartesian : ( 0.000 0.000 0.000)
Reading PDB file ...
Nr of lines read : ( 1432) Nr of atoms read : ( 1169) Centre : ( 65.687 29.626 36.810) Fractl : ( 0.811 0.366 0.454)
Checking operator : ( 1) Minimal distance (A) : ( 49.683) t1=-1 t2= 0 t3= 0
Checking operator : ( 2) Minimal distance (A) : ( 19.187) t1= 1 t2=-1 t3= 0
Checking operator : ( 3) Minimal distance (A) : ( 45.903) t1=-1 t2= 0 t3= 0
Checking operator : ( 4) Minimal distance (A) : ( 39.050) t1= 0 t2= 0 t3=-1
Checking operator : ( 5) Minimal distance (A) : ( 49.683) t1= 0 t2= 0 t3=-1
Checking operator : ( 6) Minimal distance (A) : ( 39.050) t1= 0 t2=-1 t3= 0
Checking operator : ( 7) Minimal distance (A) : ( 19.187) t1=-1 t2= 0 t3= 1
Checking operator : ( 8) Minimal distance (A) : ( 45.903) t1= 0 t2= 0 t3=-1
Checking operator : ( 9) Minimal distance (A) : ( 49.683) t1= 0 t2=-1 t3= 0
Checking operator : ( 10) Minimal distance (A) : ( 45.903) t1= 0 t2=-1 t3= 0
Checking operator : ( 11) Minimal distance (A) : ( 39.050) t1=-1 t2= 0 t3= 0
Checking operator : ( 12) Minimal distance (A) : ( 19.187) t1= 0 t2= 1 t3=-1
Nr of atoms written : ( 14028) Nr of lines written : ( 14375) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (N) c Input PDB file ? (in.pdb) Output NCS file ? (cns_ncs.def_blurb)Enter the names of all NCS operator files including the unit operator; finish with <CR> File with NCS operator(s) ? ( ) q.o ... File with NCS operator(s) ? ( ) ... SGS operator file ? (p1.sym) p43212 OSYM : (/home/gerard/oinfo/symm/) Opened file : (/home/gerard/oinfo/symm/p43212.sym) Opening O datablock : (/home/gerard/oinfo/symm/p43212.sym) ... Cell constants ? ( 100.000 100.000 100.000 90.000 90.000 90.000) 110.600 110.600 160.300 90
Shell radius (A) ? ( 5.000)
Reading PDB file ...
Nr of lines read : ( 2099) Nr of atoms read : ( 2089)
Min XYZ : ( 0.367 -44.954 -29.546) Max XYZ : ( 50.004 30.905 13.471) Centre : ( 28.234 -6.171 -7.861) Fractl : ( 0.255 -0.056 -0.049) Farthest atom : ( 246 OE1 GLU A 32 44.421 -42.326 -26.544) Distance : ( 43.798) Max centre distance : ( 92.596)
Distance : ( 89.596) New NCS op : ( 0.000 1.000 0.000 -1.000 0.000 0.000 0.000 0.000 1.000 -55.300 -55.300 -40.075) From NCS # 1 -> NCS # 1 SGS # 3 T=( -1, -1, -1) DIST = 89.6 A
...
Nr of NCSRel generated : ( 42) Nr of operators tested : ( 10976) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The output file will look like this:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----{* Created by XPAND V. 20010628/1.4 at Thu Jun 28 20:34:56 2001 for gerard *}
{=============== strict NCS (X-ray and nonbonded terms) ==============}
{* these operators are used to generate the complete asymmetric unit for structure factor and nonbonded energy calculations *}
{* NCS operator 1 *}
{* use this operator *} {+ choice: true false +} {===>} ncs_op_1=true;
{* real-space rotation matrix *} {===>} ncs_matrix_1 = ( 1.000000 0.000000 0.000000 ) ( 0.000000 1.000000 0.000000 ) ( 0.000000 0.000000 1.000000 );
{* real-space translation vector *} {===>} ncs_vector_1 = ( 0.0000 0.0000 0.0000 );
{* NCS operator 2 *}
{* use this operator *} {+ choice: true false +} {===>} ncs_op_2=true;
{* real-space rotation matrix *} {===>} ncs_matrix_2 = ( -0.700965 -0.700575 -0.133576 ) ( -0.708592 0.662871 0.241869 ) ( -0.080904 0.264192 -0.961071 );
{* real-space translation vector *} {===>} ncs_vector_2 = ( 75.4608 34.1665 -13.4335 );
{=============== strict NCS (nonbonded terms only) ==============}
{* these operators can be used to generate the full nonbonded environment around the protomer *}
{* NCS nonbonded operator 1 *}
{* from NCS # 1 -> NCS # 1 SGS # 3 T=( -1, -1, -1) DIST = 89.6 A *}
{* use this operator *} {+ choice: true false +} {===>} nb_ncs_op_1=true;
{* real-space rotation matrix *} {===>} nb_ncs_matrix_1 = ( -0.000002 -1.000000 0.000001 ) ( 1.000000 -0.000002 0.000001 ) ( -0.000001 0.000001 1.000000 );
{* real-space translation vector *} {===>} nb_ncs_vector_1 = ( -55.2999 -55.3000 -40.0749 );
{* NCS nonbonded operator 2 *}
{* from NCS # 1 -> NCS # 1 SGS # 3 T=( 0, -1, -1) DIST = 56.1 A *}
{* use this operator *} {+ choice: true false +} {===>} nb_ncs_op_2=true;
{* real-space rotation matrix *} {===>} nb_ncs_matrix_2 = ( -0.000002 -1.000000 0.000000 ) ( 1.000000 -0.000002 0.000001 ) ( -0.000001 0.000000 1.000000 );
{* real-space translation vector *} {===>} nb_ncs_vector_2 = ( 55.3001 -55.3000 -40.0750 );
... ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (N) x Input PDB file ? (in.pdb) a2u.pdb Output NCS file ? (xplor_ncs.include) ncs.includeEnter the names of all NCS operator files including the unit operator; finish with <CR>
NCS operator file 1 ? ( ) ncs1.o Opening O datablock : (ncs1.o) Datablock : (.LSQ_RT_M9A_TO_A) Data type : (R) Number : (12) Format : ((3F15.8)) ... NCS operator file 5 ? ( )
Nr of NCS operators : 4 ... SGS operator file ? (p1.sym) p212121.o Opening O datablock : (p212121.o) Datablock : (A_SYMMOP) Data type : (R) Number : (48) Format : ((3F10.4)) Nr of SGS operators : ( 4)
Nr of spacegroup symmetry operators : 4 ... Cell constants ? ( 100.000 100.000 100.000 90.000 90.000 90.000) 106.820 62.340 114.190 90.00 90.00 90.00
Margin (A) ? ( 5.000) 2
Reading PDB file ...
Nr of lines read : ( 1325) Nr of atoms read : ( 1314)
Min XYZ : ( 53.679 0.947 1.697) Max XYZ : ( 92.818 41.123 39.202) Centre : ( 72.401 20.465 22.262) Fractl : ( 0.678 0.328 0.195) Farthest atom : ( 501 OE2 GLU A 63 92.818 6.635 29.563) Distance : ( 25.718) Max centre distance : ( 53.436)
Distance : ( 50.718) New NCS op : ( -1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -1.000 106.820 -31.170 57.095) From NCS # 1 -> NCS # 1 SGS # 4 T=( 1, -1, 0) DIST = 50.7 A ... Distance : ( 38.577) NCS = XNCS : ( -0.955 0.248 -0.161 0.257 0.427 -0.867 -0.146 -0.870 -0.471 167.543 -4.093 41.981) ... Distance : ( 38.842) NCS = XNCS : ( -0.953 0.241 -0.181 0.270 0.414 -0.869 -0.135 -0.878 -0.460 167.320 -3.427 43.549)
Distance : ( 35.837) New NCS op : ( 0.953 -0.241 -0.181 -0.270 -0.414 -0.869 0.135 0.878 -0.460 -7.090 65.767 -13.546) From NCS # 4 -> NCS # 3 SGS # 4 T=( 1, 1, -1) DIST = 35.8 A
Nr of NCS operators : 1
NCSOP 1 = 0.9533499 -0.2702062 0.1345823 -7.090 -0.2412489 -0.4140138 0.8777195 65.767 -0.1814464 -0.8692417 -0.4598870 -13.546 Determinant of rotation matrix = 1.000000 Crowther Alpha Beta Gamma 81.28262 117.37982 -78.20933 Spherical polars Omega Phi Chi 89.06552 169.74599 117.40488 Direction cosines of rotation axis -0.98390 0.17799 0.01631 Dave Smith -117.65260 100.45403 15.82423 Rotation angle = 117.404884
Nr of NCSRel generated : ( 22) Nr of operators tested : ( 12005) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- REMARK Created by XPAND V. 941219/0.3 at Tue Dec 20 01:49:21 1994 for user gerard{ Invoke strict non-crystallographic symmetry }
ncs strict
{ ==> Assuming identity skew matrix }
skew matrix = ( 1.000000 0.000000 0.000000 ) ( 0.000000 1.000000 0.000000 ) ( 0.000000 0.000000 1.000000 ) translation = ( 0.0000 0.0000 0.0000 ) end
xncsrel { # 1 } matrix = ( 1.000000 0.000000 0.000000 ) = ( 0.000000 1.000000 0.000000 ) = ( 0.000000 0.000000 1.000000 ) translation = ( 0.0000 0.0000 0.0000 ) end { xncsrel # 1 }
...
{ xncsrel end }
ncsrel { # 1 } { from NCS # 1 -> NCS # 1 SGS # 4 T=( 1, -1, 0) DIST = 50.7 A } matrix = ( -1.000000 0.000001 0.000000 ) = ( 0.000001 1.000000 0.000001 ) = ( 0.000000 0.000001 -1.000000 ) translation = ( 106.8200 -31.1701 57.0950 ) end { ncsrel # 1 }
ncsrel { # 2 } { from NCS # 1 -> NCS # 1 SGS # 4 T=( 1, 0, 0) DIST = 50.7 A } matrix = ( 1.000000 0.000001 -0.000008 ) = ( 0.000001 -1.000000 0.000001 ) = ( -0.000008 -0.000001 -1.000000 ) translation = ( 160.2302 31.1699 0.0005 ) end { ncsrel # 2 }
...
ncsrel { # 22 } { from NCS # 4 -> NCS # 3 SGS # 4 T=( 1, 1, -1) DIST = 35.8 A } matrix = ( 0.953350 -0.270206 0.134582 ) = ( -0.241249 -0.414014 0.877720 ) = ( -0.181446 -0.869242 -0.459887 ) translation = ( -7.0905 65.7665 -13.5464 ) end { ncsrel # 22 }
{ ncsrel end }
?
end {ncs strict} ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If you don't have NCS, supply the identity operator as the only "NCS operator". The contacts are classified by the program if they involve only C, N, O and S atoms (using a set of simple hard-coded rules). Interactions between symmetry-related copies of a residue (same residue type, number, chain and insert) are flagged with the word "SELF".
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (N) b Input PDB file ? (in.pdb) a2u.pdbEnter the names of all NCS operator files including the unit operator; finish with <CR>
NCS operator file 1 ? ( ) ncs1.o Opening O datablock : (ncs1.o) ... SGS operator file ? (p1.sym) p212121.o Opening O datablock : (p212121.o) ... Cell constants ? ( 100.000 100.000 100.000 90.000 90.000 90.000) 106.820 62.340 114.1
Enter maximum distance for NCS+SGS interactions E.g., 2.4 A for bad contacts, 3.6 A for hydrogen bonds and salt links, or 4.5 A to include hydrophobic interactions Max contact distance (A) ? ( 5.000)
Reading PDB file ...
Nr of lines read : ( 1325) Nr of atoms read : ( 1314)
Min XYZ : ( 53.679 0.947 1.697) Max XYZ : ( 92.818 41.123 39.202) Centre : ( 72.401 20.465 22.262) Fractl : ( 0.678 0.328 0.195) Farthest atom : ( 501 OE2 GLU A 63 92.818 6.635 29.563) Distance : ( 25.718) Max centre distance : ( 56.436)
From NCS # 1 -> NCS # 1 SGS # 3 T=( 1, -1, 0) DIST = 50.7 A Pure SGS interaction Nr of contacts : ( 0) ...
From NCS # 1 -> NCS # 4 SGS # 1 T=( 0, 0, 0) DIST = 33.4 A Mixed NCS and SGS interaction CD GLU A 49 ---> OD1 ASN A 110 = 4.55 A - OE1 GLU A 49 ---> OD1 ASN A 110 = 3.86 A - OE2 GLU A 49 ---> OD1 ASN A 110 = 4.88 A - CB ASN A 50 ---> CE2 PHE A 108 = 4.80 A - CG ASN A 50 ---> CD2 PHE A 108 = 4.81 A - CG ASN A 50 ---> CE2 PHE A 108 = 4.41 A hydrophobic interaction ... OD1 ASN A 50 ---> CE2 PHE A 108 = 3.58 A ==> (too ?) close contact ! ... OD1 ASN A 50 ---> N ASN A 110 = 3.20 A potential hydrogen bond ? OD1 ASN A 50 ---> CA ASN A 110 = 3.79 A ? ... OE1 GLU A 79 ---> OE1 GLU A 79 = 4.90 A SELF - OE1 GLU A 79 ---> O1 HOH B 212 = 4.61 A - OE1 GLU A 79 ---> OE2 GLU A 76 = 4.60 A - CB PHE A 81 ---> CB PHE A 81 = 4.42 A SELF hydrophobic interaction CB PHE A 81 ---> CG PHE A 81 = 4.05 A SELF hydrophobic interaction CB PHE A 81 ---> CD1 PHE A 81 = 4.17 A SELF hydrophobic interaction CB PHE A 81 ---> CE1 PHE A 81 = 4.53 A SELF - ... O1 HOH B 227 ---> CD LYS A 153 = 1.88 A ==> BAD contact ! ... NH1 ARG A 29 ---> NZ LYS A 124 = 3.51 A ==> (too ?) close positive charges ? ... OD1 ASP A 77 ---> OE2 GLU A 2 = 3.22 A ==> (too ?) close negative charges ? ... From NCS # 4 -> NCS # 3 SGS # 4 T=( -1, 1, 0) DIST = 48.3 A Mixed NCS and SGS interaction Nr of contacts : ( 0)
Total nr of contacts : ( 4270) Every contact should occur twice ! ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
If you have many waters, you can write the output to a log file instead of to the screen (version 1.1).
If you want to use XPAND as a "filter" to screen potential waters picked in a difference map, you can write out all waters except those that appear not to be tightly bound (but note that symmetry is not taken into account) to a new PDB file (version 1.1).
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (N) w Input PDB file ? (in.pdb) 1cbs_sphere.pdb Log file (RETURN for screen output) ? ( ) Output PDB file (RETURN to skip) ? ( )Max interaction distance : ( 3.400) Min bad-charge distance : ( 3.000) Max good-charge distance : ( 2.400) Min contact distance : ( 1.800)
Reading PDB file ...
Nr of lines read : ( 3610) Nr of atoms read : ( 3600)
=> Water # 1 = HOH- 300 atom O Nbr ARG- 111- NE @ 3.12 A Nbr HOH- 309- O @ 2.74 A Nr + charges 0 | Nr - charges 0 Nr Hb donors 0 | Nr Hb accept 0 | Nr don/acc 2 Nr CYS S 0 | Nr MET S 0 This could be HOH
=> Water # 2 = HOH- 301 atom O Nbr LYS- 66- N @ 2.88 A Nbr LYS- 66- O @ 3.35 A Nbr GLU- 69- O @ 2.87 A Nbr HOH- 335- O @ 2.81 A Nr + charges 0 | Nr - charges 0 Nr Hb donors 1 | Nr Hb accept 2 | Nr don/acc 1 Nr CYS S 0 | Nr MET S 0 This could be HOH ... => Water # 12 = HOH- 311 atom O Nbr LYS- 30- O @ 2.84 A Nr + charges 0 | Nr - charges 0 Nr Hb donors 0 | Nr Hb accept 1 | Nr don/acc 0 Nr CYS S 0 | Nr MET S 0 Does *not* look like a tightly bound water ! ... => Water # 302 = HOH- Z 397 atom O Nbr ARG- Z 29- NH2 @ 3.07 A Nbr HOH- Z 387- O @ 3.14 A Nbr GLU- Z 69- OE2 @ 3.22 A Nr + charges 1 | Nr - charges 1 Nr Hb donors 1 | Nr Hb accept 1 | Nr don/acc 1 Nr CYS S 0 | Nr MET S 0 This could be HOH
Nr of waters scrutinized : ( 302) # ? NH4+ (or other small cation with H) : ( 0) # ? F- (or other small anion) : ( 0) # ? Na+ (or other small monovalent cation) : ( 0) # ? Mg++ (or other small divalent cation) : ( 0) # ? HOH (with reasonable neighbours) : ( 229) # non-tightly bound water molecules : ( 73)
Task ? (W) q ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (N) w Input PDB file ? (in.pdb) /nfs/pdb/full/1cbs.pdb Log file (RETURN for screen output) ? ( ) 1cbs_waters.log Output PDB file (RETURN to skip) ? ( ) 1cbs_ok.pdbMax interaction distance : ( 3.500) Min bad-charge distance : ( 3.500) Max good-charge distance : ( 2.800) Min contact distance : ( 1.800)
Reading PDB file ...
Nr of lines read : ( 1459) Nr of atoms read : ( 1213)
Nr of waters scrutinized : ( 100) # ? NH4+ (or other small cation with H) : ( 1) # ? F- (or other small anion) : ( 3) # ? Na+ (or other small monovalent cation) : ( 2) # ? Mg++ (or other small divalent cation) : ( 0) # ? HOH (with reasonable neighbours) : ( 71) # non-tightly bound water molecules : ( 26) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (N) m Output MTRIX file ? (out.pdb) mtrix.pdbEnter the names of all NCS operator files including the unit operator; finish with <CR>
NCS operator file 1 ? ( ) ncs1.o Opening O datablock : (ncs1.o) Datablock : (.LSQ_RT_M9A_TO_A) Data type : (R) Number : (12) Format : ((3F15.8))
...
NCS operator file 5 ? ( )
Nr of NCS operators : 4
NCSOP 1 = 1.0000000 0.0000000 0.0000000 0.000 0.0000000 1.0000000 0.0000000 0.000 0.0000000 0.0000000 1.0000000 0.000 Determinant of rotation matrix 1.000000 ... Dave Smith -2.40361 -76.69563 -166.60451 Rotation angle 179.154190
Task ? (M) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The generated file may look as follows:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- REMARK REMARK NCS MTRX CARDS REMARK GENERATED BY : XPAND REMARK VERSION : 951022/0.7 REMARK DATE : Mon Oct 30 18:19:29 1995 REMARK MTRIX1 1 1.000000 0.000000 0.000000 0.00000 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 MTRIX1 2 -0.955168 0.257340 -0.146391 167.54320 MTRIX2 2 0.248227 0.426599 -0.869711 -4.09250 MTRIX3 2 -0.161362 -0.867058 -0.471352 41.98070 MTRIX1 3 -0.994267 -0.046533 -0.096268 176.73730 MTRIX2 3 -0.065414 -0.447478 0.891899 27.41760 MTRIX3 3 -0.084580 0.893083 0.441869 -5.85930 MTRIX1 4 0.947451 -0.225636 0.226772 7.42830 MTRIX2 4 -0.222216 -0.974142 -0.040846 58.26170 MTRIX3 4 0.230124 -0.011693 -0.973091 -5.61790 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (N) o Input PDB file ? (in.pdb) 2bny.pdb Output file with NCS operator(s) ? ( ) mtrix.rt MTRIX nr : ( 1) MTRIX nr : ( 2)[...]
MTRIX nr : ( 10) Nr of lines read : ( 4317) Operators read : ( 10) Writing : (.LSQ_RT_1) Writing : (.LSQ_RT_2)
[...]
Writing : (.LSQ_RT_10) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Use this command to extract and convert the BIOMT operators from a PDB file. Subsequently, generate the complete biologically relevant assembly with the option "N" of this program.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (O) r Input PDB file ? (2bny.pdb) Output file with NCS operator(s) ? ( ) biomt.rt BioMT nr : ( 1) BioMT nr : ( 2)[...]
BioMT nr : ( 60) Nr of lines read : ( 4317) Operators read : ( 60) Writing : (.LSQ_RT_1) Writing : (.LSQ_RT_2)
[...]
Writing : (.LSQ_RT_60) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Generating the entire assembly (in this case, a virus particle) with the "N" option:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (R) n Input PDB file ? (2bny.pdb) 2bny_ca.pdb Output PDB file ? (out.pdb) biomt.pdbEnter the names of the O-style NCS operator files including the unit operator; finish with <CR> File with NCS operator(s) ? ( ) biomt.rt
[...]
==> Read NCS operator : (.LSQ_RT_60)
Nr of RT operators : 1
RT-OP 1 = -0.5000030 -0.6455010 0.5773450 0.000 -0.6454900 -0.1666690 -0.7453520 0.000 0.5773500 -0.7453630 -0.3333360 0.000 Determinant of rotation matrix 1.000000 Column-vector products (12,13,23) 0.000000 -0.000008 0.000007 ERROR --- WARNING - Non-orthogonal column vectors Crowther Alpha Beta Gamma 127.761 -109.471 52.239 Spherical polars Omega Phi Chi 54.736 -52.239 179.838 Direction cosines of rotation axis 0.499999 -0.645496 0.577349 X-PLOR polars Phi Psi Kappa 45.155 -107.845 180.000 Lattmann Theta+ Theta2 Theta- 180.000 109.471 -104.478 WARNING - cosine of rot angle not in [-1,+1] : ( -1.000) Reset to : ( -1.000) Rotation angle 180.000
Nr of NCS operators now : ( 60) File with NCS operator(s) ? ( )
Select: A = automatic generation of chain IDs M = enter chain IDs manually Option (A/M) ? (A)
Reading PDB file ...
Nr of lines read : ( 407) Nr of atoms read : ( 387)
NCS expansion for operator # 1 with chain ID |A| NCS expansion for operator # 2 with chain ID |B|
[...]
NCS expansion for operator # 60 with chain ID |H|
Nr of atoms generated : ( 23220) Nr of lines written : ( 23661) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (N) i Output RT file ? (inverted.rt)Enter the names of all NCS operator files including the unit operator; finish with <CR> File with NCS operator(s) ? ( ) q.o
==> Read NCS operator : (.LSQ_RT_UNIT)
Nr of RT operators : 1
[...]
Nr of NCS operators now : ( 2) File with NCS operator(s) ? ( )
***** Operator nr 1 *****
Nr of RT operators : 1
RT-OP 1 = 1.0000000 0.0000000 0.0000000 0.000 0.0000000 1.0000000 0.0000000 0.000 0.0000000 0.0000000 1.0000000 0.000 Determinant of rotation matrix 1.000000 Column-vector products (12,13,23) 0.000000 0.000000 0.000000 Crowther Alpha Beta Gamma 0.000 0.000 0.000 Spherical polars Omega Phi Chi 0.000 *undefined* 0.000 Direction cosines of rotation axis 0.000000 0.000000 0.000000 X-PLOR polars Phi Psi Kappa *undefined* *undefined* 0.000 Lattmann Theta+ Theta2 Theta- *undefined* 0.000 *undefined* Rotation angle 0.000
***** INVERSE Operator nr 1 *****
Nr of RT operators : 1
RT-OP 1 = 1.0000000 0.0000000 0.0000000 0.000 0.0000000 1.0000000 0.0000000 0.000 0.0000000 0.0000000 1.0000000 0.000 Determinant of rotation matrix 1.000000 Column-vector products (12,13,23) 0.000000 0.000000 0.000000 Crowther Alpha Beta Gamma 0.000 0.000 0.000 Spherical polars Omega Phi Chi 0.000 *undefined* 0.000 Direction cosines of rotation axis 0.000000 0.000000 0.000000 X-PLOR polars Phi Psi Kappa *undefined* *undefined* 0.000 Lattmann Theta+ Theta2 Theta- *undefined* 0.000 *undefined* Rotation angle 0.000
***** Operator nr 2 *****
Nr of RT operators : 1
RT-OP 1 = -0.7009653 -0.7005748 -0.1335759 75.461 -0.7085917 0.6628705 0.2418688 34.167 -0.0809036 0.2641924 -0.9610707 -13.434 Determinant of rotation matrix 1.000000 Column-vector products (12,13,23) 0.000000 0.000000 0.000000 Crowther Alpha Beta Gamma 118.910 163.960 72.974 Spherical polars Omega Phi Chi 97.977 -67.032 178.345 Direction cosines of rotation axis 0.386420 -0.911755 -0.138772 X-PLOR polars Phi Psi Kappa -160.246 24.243 178.345 Lattmann Theta+ Theta2 Theta- -191.884 163.960 -134.063 Rotation angle 178.345
***** INVERSE Operator nr 2 *****
Nr of RT operators : 1
RT-OP 1 = -0.7009654 -0.7085918 -0.0809037 76.019 -0.7005748 0.6628705 0.2641924 33.767 -0.1335759 0.2418687 -0.9610708 -11.095 Determinant of rotation matrix 1.000000 Column-vector products (12,13,23) 0.000000 0.000000 0.000000 Crowther Alpha Beta Gamma 107.026 163.960 61.090 Spherical polars Omega Phi Chi 82.022 112.968 178.345 Direction cosines of rotation axis -0.386477 0.911884 0.138794 X-PLOR polars Phi Psi Kappa 19.755 -24.243 178.345 Lattmann Theta+ Theta2 Theta- -168.116 163.960 -134.063 Rotation angle 178.345
Nr of NCS operators written : ( 2) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The original operators:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
.lsq_rt_unit R 12 (3f15.7)
1.0000000 0.0000000 0.0000000
0.0000000 1.0000000 0.0000000
0.0000000 0.0000000 1.0000000
0.0000000 0.0000000 0.0000000
.lsq_rt_m7a_tom7b r 12 (3f15.7)
-0.7009653 -0.7085917 -0.0809036
-0.7005748 0.6628705 0.2641924
-0.1335759 0.2418688 -0.9610707
75.4608154 34.1665306 -13.4335337
! Created by LSQMAN V. 931027/1.1 at Wed Nov 3 19:04:00 1993 for user gerard
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
The inverted operators:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
! Created by XPAND V. 031223/1.5 at Tue Dec 23 20:00:56 2003 for gerard
!
.LSQ_RT_1 R 12 (3f15.8)
1.00000000 0.00000000 0.00000000
0.00000000 1.00000000 0.00000000
0.00000000 0.00000000 1.00000000
0.00000000 0.00000000 0.00000000
!
.LSQ_RT_2 R 12 (3f15.8)
-0.70096540 -0.70057476 -0.13357593
-0.70859176 0.66287047 0.24186872
-0.08090368 0.26419240 -0.96107078
76.01872253 33.76699829 -11.09464264
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (N) Defaults Input PDB file ? (in.pdb) ../structures/1cbs_holo_crabp_ii.pdbReading PDB file ... CRYST1 card found : (CRYST1 45.650 47.560 77.610 90.00 90.00 90.00 P 21 21 21 4 1CBS 216) Cell axes (A) : ( 45.650 47.560 77.610) Cell angles (deg) : ( 90.000 90.000 90.000) Spacegroup name : (P 21 21 21) SGS operator file : (p212121.sym) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
- all SGS and NCS operators must be in O datablock format
- extra REMARK cards are added to the output PDB files to mark the start of new NCS/SGS-related molecules/atoms
- if you plan to use an option which produces a lot of output, use the Unix "tee" command to copy the output both to the screen and to a file: run xpand |& tee xpand.log
None, at present.
Created at Wed Apr 27 17:56:04 2005
by MAN2HTML version 050114/2.0.6 . This manual
describes XPAND, a program of the Uppsala
Software Factory (USF), written and maintained by Gerard Kleywegt. © 1992-2005.