Program : XPAND
Version : 981124
Author : Gerard J. Kleywegt, Dept. of Cell and Molecular Biology,
Uppsala University, Biomedical Centre, Box 590,
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 (1992-1999). Uppsala University, Uppsala, Sweden. Unpublished program.
* 2 * G.J. Kleywegt & T.A. Jones (1999 ?). Chapter 25.2.6. O and associated programs. Int. Tables for Crystallography, Volume F. To be published.
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)
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.
- 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".
- 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.
- 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
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 ----- % 455 gerard rigel 19:39:23 progs/xpand > XPAND*** XPAND *** XPAND *** XPAND *** XPAND *** XPAND *** XPAND *** XPAND ***
Version - 941219/0.3 (C) 1993/4 Gerard J. Kleywegt, Dept. Mol. Biology, BMC, Uppsala (S) 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, etc. etc.
Started - Fri May 13 19:41:03 1994 User - gerard Mode - interactive Host - rigel ProcID - 15374 Tty - /dev/ttyq19
*** XPAND *** XPAND *** XPAND *** XPAND *** XPAND *** XPAND *** XPAND ***
Max nr of input atoms = ( 50000) Max nr of SGS operators = ( 96) Max nr of NCS operators = ( 96)
==> 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 X = generate complete X-PLOR (X)NCS file B = generate non-bonded contacts (NCS+SGS) ? = 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 -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Task ? (P) f Input PDB file ? (cas.pdb) Output PDB file ? (qq.pdb) casunit.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
...
Cell constants ? ( 106.820 62.340 114.190 90.000 90.000 90.000) Max allowed fractional range [0,+1> Fractional lower limits ? ( 0.000 0.000 0.000) Fractional upper limits ? ( 1.000 1.000 1.000) 1 .5 .5
Reading PDB file ...
Nr of lines read : ( 648) Nr of atoms read : ( 632)
Min XYZ : ( 55.465 -13.334 -28.111) Max XYZ : ( 118.672 50.560 38.472) Centre : ( 87.728 19.608 7.400) Fractl : ( 0.821 0.315 0.065) Farthest atom : ( 4885 CA ASP D 133 67.647 18.695 -27.094) Distance : ( 39.923) Max centre distance : ( 83.847)
Checking operator : ( 1) Translation applied : ( 0.000 0.000 0.000)
Checking operator : ( 2) Does not fit into fractional range
Checking operator : ( 3) Does not fit into fractional range
Checking operator : ( 4) Does not fit into fractional range
Nr of atoms written : ( 632) Nr of lines written : ( 655) ----- 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 -----
----- 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 -----
----- 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 -----
- 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 Fri Dec 18 19:42:28 1998
by MAN2HTML version 971024/1.6