Assuming that the executable is in your PATH (or that you have a symbol defined for it), and that its name is Qs, go to the /my_dirs/Qs/example/ directory, make your window at least 80 characters wide, and type Qs example.in. What you should see on your terminal should be similar to this :
host# Qs example.in
QQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ
QQQQQQQQQQQQQQQQQQQQQQ QQQQQQ QQQQQQQQQQQQQQQQQQQQQQ
QQQQQQQQQQQQQQQQQQQQQ QQQQ QQQQQQQQQQQQQQQQQQQQQ
QQQQQQQQQQQQQQQQQQQ QQQQ QQQQQQQQQQQQQQQQQQQ
QQQQQQQQQQQQQQQQQ QQQQ QQQQQQQQQQQQQQQQQ
QQQQQQQQQQQQQ QQQQQQ QQQQQQQQQQQQQ
QQQQQQ QQQQQQ QQQQQQ
QQQQQQQQ
QQQQQQQQQQ
QQQQQQQQQQQQ
QQQQQQQQQQQQ
QQQQQQQQQQ
QQQQQQ
Queen of Spades
Version 1.3
_______________________________________________________________________________
#
# Example script for testing Qs
#
TARGET R-FACTOR
CYCLES 3
STEPS 100000
STARTING_T 0.01500
FINAL_T 0.00500
INFO 1000
NOISE_ADDED 0.20
RESOLUTION 150.0 4.0
AMPLIT_CUTOFF 500.0
SIGMA_CUTOFF 0.0
RANDOM_SELECT 1.0
FREE 0.20
MODEL example.pdb
DATA example.hkl
GLOBAL_B 20.0
MOLECULES 1
SEED 357539
SCALECELL 4.0
MAXGRIDSPACING 1.0
SCMODE wilson
INTERPOLATION linear
POSTSCRIPT colour
CELL 103.900 38.700 34.000 90.000 100.600 90.000
GROUP 5
_______________________________________________________________________________
Minimisation performed against the R-factor.
Will perform 3 independent minimisations.
Number of steps for minimisation : 100000
Information about the minimisation will be printed every 1000 moves.
Noise added to Fs : max fraction 0.20000
Resolution limits set to 150.00 - 4.00 Angstrom.
Amplitude cutoff set to 500.00
Reflections with F/sigma(F) less than 0.00, will be rejected.
Only a fraction 1.000 of the available reflections will be used.
Free value will be calculated over a fraction 0.200 of the data set.
Model PDB file name set to example.pdb
Reflection file name set to example.hkl
Global temperature factor for model set to 20.000000
Number of molecules in asymmetric unit : 1
Random number generator reset to 357539
Initial scale value set to 4.00
Maximum grid spacing (in Angstrom) is 1.000000
Wilson-like scaling will be used.
Will be using linear interpolation.
Colour postscript output requested.
Cell parameters 103.90 38.70 34.00 90.00 100.60 90.00
Space group 5 with 2 symmetry operators
Symmetry operator :
-1 +0 +0
+0 +1 +0
+0 +0 -1
with translation vector : +0.0000000 +0.0000000 +0.0000000
2 symmetry operators read in.
Space group given. Lattice type is C (only used for the packing diagrams).
Target function for minimisation : R-factor
No bulk-solvent correction requested.
Temperature control :
Temperature is linearly dependent on time, and will be
decreased from To at t=0, to Tt at t=100000.
Move size control :
The modulus of the moves attempted is linearly dependent on the current
R-factor (or correlation) and time, with maximum possible values of
180.00 degrees for the kappa angle, and 0.5000 fractional units
for any of the translations.
_______________________________________________________________________________
Reading atoms ... 994 atoms read (0 unknown)
Centre of mass at -3.272 30.256 33.689
Box dimensions (A) : 31.760 43.723 33.092 along x,y,z
Translating/rotating ... done.
Centre of mass at -0.000 0.000 -0.000
Box dimensions (A) : 45.112 31.867 28.035 along x,y,z
Reading reflections ... 414 read.
Reflections for free value 81
Excluded reflections 2351
Lowest resolution reflection : 51.1 Angstrom
Highest resolution reflection : 4.0 Angstrom
Big cell : 180.448 127.467 112.140
Grid 192 128 120
with spacing 0.940 0.996 0.934
Allocate memory ... done.
FFTW is learning how to do FFTs ... done.
Saving FFTW's wisdom file ... done.
Atomic density profiles (B=20.0) ... done.
Make electron density map ... done.
Write out projections ... done.
Calculate molecular transform ... done in 1 seconds.
Rearranging transform ... done.
Write out central sections ... done.
Initialisations ... done.
Ready to roll after ... 4 seconds.
_______________________________________________________________________________
Starting minimisation 1.
Initial R-factor 0.64758
Starting free value 0.52872
$TABLE: Qs simulation 1:
$GRAPHS
:R vs time:A:1,2:
:Rfree vs time:A:1,3:
:Temp vs time:A:1,4:
:R & Rf vs time:A:1,2,3:
$$
TIME R-FACTOR FREE TEMP
$$
$$
1000 0.558826 0.576907 0.014900
2000 0.574403 0.564562 0.014800
3000 0.558421 0.565640 0.014700
...........................................
100000 0.321598 0.384552 0.005000
$$
Best solution had a R-factor (or 1-Corr) of 0.30767
Few cycles down the gradient starting from best solution ...
Starting R-factor (or 1-Corr) 0.30767
Starting free value ... 0.36779
91000 0.308809 0.369162 0.000900
92000 0.309151 0.368926 0.000800
93000 0.308709 0.369571 0.000700
94000 0.308692 0.368035 0.000600
95000 0.308307 0.365925 0.000500
96000 0.308363 0.365070 0.000400
97000 0.308948 0.364910 0.000300
98000 0.308106 0.364235 0.000200
99000 0.307692 0.365615 0.000100
100000 0.307527 0.365723 0.000000
Done the minimisation in ... 145 seconds.
Best solution had a R-factor (or 1-Corr) of 0.30730
Starting minimisation 2.
Initial R-factor 0.61194
Starting free value 0.62831
$TABLE: Qs simulation 2:
$GRAPHS
:R vs time:A:1,2:
:Rfree vs time:A:1,3:
:Temp vs time:A:1,4:
:R & Rf vs time:A:1,2,3:
$$
TIME R-FACTOR FREE TEMP
$$
$$
1000 0.566813 0.567553 0.014900
..........................................
Normally, at least one of the minimisations is expected to converge to the correct solution (with an R-factor of about 30%).