In the directory where the data.hkl and model.pdb (or model?.pdb) files are --and assuming that the symbol Qs has been defined (as discussed in the installation section), give : 11Qs -auto <xxx> where <xxx> is the total number of search models per asymmetric unit of the target structure, or Qs -reso <low> <high> -auto <xxx> if you want to explicitly define resolution limits (for example, Qs -auto 1 or Qs -reso 20 4 -auto 2, etc.).12The program will do its best to determine parameters suitable for the given problem, and if it succeeds, it will start the calculation. The name of the game in this procedure is memory : if the physical memory of your system is adequate for storing the whole molecular transform (or transforms in the multi-model case), then you can stop the program and submit it as a batch job. If, on the other hand, QS allocated 128 MBytes of memory when only 64 MBytes of it is physical memory, the program will never start : it will endlessly be reading and writing to the swap space on the disk with no chance of even finishing the FFT step. If that's the case, you will probably have to reduce the resolution of your data and try again. What I suggest you do, is to run the program interactively till it gets past the FFT stage. For medium-sized proteins and with adequate physical memory, this should only take a few minutes (or even seconds). If on the other hand the physical memory is not enough, the program will get stuck in the electron density calculation and FFT steps. What you should see (in the case of a multi-model problem) should look similar to this :
host# Qs -reso 50 4 -auto 3
QQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ
QQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQQ
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
_______________________________________________________________________________
############################################################
## ##
## Automatically created by Qs ##
## ##
############################################################
############################################################
#
# Target function (can be R-FACTOR, CORR-1 or CORR-2) and
# number of minimisations and steps.
#
TARGET CORR-1
CYCLES 5
STEPS 30000000
############################################################
#
# Annealing schedule & move size control.
# This is for a Boltzmann annealing schedule with a constant
# move-size and a fixed starting temperature.
#
BOLTZMANN
STARTING_TEMP 0.0700
############################################################
#
# Reflection selection.
#
KEEP 0.70
AMPLIT_CUTOFF 1.0
SIGMA_CUTOFF 2.0
RESOLUTION 50.00 4.00
RANDOM_SELECT 1.0
############################################################
#
# Fraction of reflections for free set.
#
FREE 0.10
############################################################
#
# Files to use for reading model(s) and data.
#
MOD1 model1.pdb
MOD2 model2.pdb
MOD3 model3.pdb
DATA data.hkl
############################################################
#
# Scales, grid, random number generator seed, B-factors etc.
#
GRAUTO
SCMODE wilson
INTERPOLATION linear
SEED 47579
B_M1 20.00
B_M2 20.00
B_M3 20.00
############################################################
#
# Log file and postscript-related things.
#
INFO 1000
POSTSCRIPT colour
############################################################
#
# Finally, cell, space group and molecules per a.u.
#
CELL 64.660 85.460 83.370 90.000 112.030 90.000
GROUP 4
MOLECULES 3
#
#
############################################################
_______________________________________________________________________________
Minimisation performed against the 1-Corr(Fo,Fc) target.
Will perform 5 independent minimisations.
Number of steps for minimisation : 30000000
Fraction of strongest reflections to keep : 0.700000
Amplitude cutoff set to 1.00
Reflections with F/sigma(F) less than 2.00, will be rejected.
Resolution limits set to 50.00 - 4.00 Angstrom.
Only a fraction 1.000 of the available reflections will be used.
Free value will be calculated over a fraction 0.100 of the data set.
Model number 1 : PDB file name set to model1.pdb
Model number 2 : PDB file name set to model2.pdb
Model number 3 : PDB file name set to model3.pdb
Reflection file name set to data.hkl
Will try to determine SCALE and MAXGRIDSPACING automatically.
Wilson-like scaling will be used.
Will be using linear interpolation.
Random number generator reset to 47579
Model number 1 : overall B-factor set to 20.000000
Model number 2 : overall B-factor set to 20.000000
Model number 3 : overall B-factor set to 20.000000
Information about the minimisation will be printed every 1000 moves.
Colour postscript output requested.
Cell parameters 64.66 85.46 83.37 90.00 112.03 90.00
Space group 4 with 2 symmetry operators
Symmetry operator :
-1 +0 +0
+0 +1 +0
+0 +0 -1
with translation vector : +0.0000000 +0.5000000 +0.0000000
Number of molecules in asymmetric unit : 3
2 symmetry operators read in.
Space group given. Lattice type is P (only used for the packing diagrams).
Target function for minimisation : 1.0-Corr(Fo,Fc)
No bulk-solvent correction requested.
Temperature control :
Boltzmann scaling selected : the temperature at each step (k)
will be given by T=T0/ln(k). T0 is set to the value defined by
the keyword STARTing_temp.
Move size control :
The modulus of the moves attempted is constant and independent of
either time or R-factor (or correlation). Its maximum value only
depends on the resolution of the input data.
_______________________________________________________________________________
Reading atoms (Model 1) 2240 atoms read (0 unknown)
Centre of mass at 19.749 23.683 64.488
Box dimensions (A) : 57.433 58.288 56.652 along x,y,z
Translating/rotating ... done.
Centre of mass at 0.000 0.000 -0.000
Box dimensions (A) : 65.001 51.063 50.244 along x,y,z
Reading atoms (Model 2) 869 atoms read (0 unknown)
Centre of mass at 39.417 33.807 65.919
Box dimensions (A) : 49.416 32.517 81.659 along x,y,z
Translating/rotating ... done.
Centre of mass at 0.000 0.000 -0.000
Box dimensions (A) : 85.850 41.229 27.084 along x,y,z
Reading atoms (Model 3) 814 atoms read(0 unknown,38 P->S)
Few or no CA atoms. Packing diagrams will include all atoms (keyword PACKall).
Centre of mass at 37.756 36.302 41.899
Box dimensions (A) : 75.250 22.857 24.875 along x,y,z
Translating/rotating ... done.
Centre of mass at -0.000 -0.000 0.000
Box dimensions (A) : 75.564 22.832 25.470 along x,y,z
Calculating |F| cutoff ... 112.70
Reading reflections ... 4943 read.
Reflections for free value 525
Excluded reflections 17136
Lowest resolution reflection : 19.5 Angstrom
Highest resolution reflection : 4.0 Angstrom
Scale set to 4.000
Big cell : 343.400 204.253 200.977
Grid 384 210 210
with spacing 0.894 0.973 0.957
Physical memory required 193 MBytes
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 (Model 1) ... done.
Atomic density profiles (B=20.0) ... done.
Make electron density map (Model 2) ... done.
Atomic density profiles (B=20.0) ... done.
Make electron density map (Model 3) ... done.
Write out projections ... done.
Calculate molecular transform (1) ... done in 5 seconds.
Calculate molecular transform (2) ... done in 5 seconds.
Calculate molecular transform (3) ... done in 5 seconds.
Rearranging transforms ... done.
Write out central sections ... done.
Initialisations ... done.
Ready to roll after ... 72 seconds.
_______________________________________________________________________________
Starting minimisation 1.
Initial 1-Corr(Fo,Fc) 0.94847
Starting free value 0.88592
$TABLE: Qs simulation 1:
$GRAPHS
:1-C(Fo,Fc) vs time:A:1,2:
:Free 1-C(Fo,Fc) vs time:A:1,3:
:Temp vs time:A:1,4:
:1-C(Fo,Fc) & Free vs time:A:1,2,3:
$$
TIME 1-C(Fo,Fc) FREE TEMP
$$
$$
1000 0.931011 0.921275 0.010132
2000 0.921983 0.927676 0.009209
3000 0.924896 0.916017 0.008743
4000 0.922867 0.919347 0.008440
..........................................
You can now stop the program, and submit a proper batch job : for unix something like
batch /usr/local/bin/Qs -reso 50 4 -auto 3 > LOG <CTRL-D>and for VMS :
submit/noprint/notify/queue=for_ever/log=dsk$23:[my.dir]QS.LOG Qs.comwhere the Qs.com looks like
$ set def dsk$21:[my.directory] $ $ Qs :== $dsk$56:[Qs.directory]Qs-dec4000-vms6.exe $ Qs -auto 1 $ $ exit