Qs (Queen of Spades) |
Queen of Spades is a "brute force" style molecular replacement program which uses a method based on a reverse Monte Carlo minimisation of the conventional crystallographic R-factor in the 6n-dimensional space defined by the rotational and translational parameters of the n molecules. Because all parameters of all molecules are determined simultaneously, this algorithm should improve the signal-to-noise ratio in difficult cases involving high crystallographic/non-crystallographic symmetry in tightly packed crystal forms.
Because a successful run of this application can last weeks or months on a single processor, it is best used in parallel fashion on the biowulf cluster. It should not be the first application to try for molecular replacement (try AMoRe instead, for example), but rather as a last resort.
Version: 1.3
Author: Nicholas M. Glykos
How to use
Minimally, you need three files for a single model per asymmetric unit: a pdb file containing the coordinates of the model, the data in hkl format, and a parameter input file.
Qs_test.pdb:
ATOM 1 N LYS 1 -11.460 31.361 22.771 1.00 20.48 N ATOM 2 CA LYS 1 -11.083 30.241 21.810 1.00 20.62 C ATOM 3 C LYS 1 -11.021 29.061 22.764 1.00 20.27 C ATOM 4 O LYS 1 -10.316 29.368 23.686 1.00 20.31 O ATOM 5 CB LYS 1 -9.766 30.428 21.114 1.00 20.34 C ...
Qs_test.hkl:
-34 0 1 173.60 1.00 -34 0 2 548.05 1.00 -34 0 3 137.69 1.00 -34 0 4 229.47 1.00 -34 2 1 188.31 1.00 ...
Qs_test.in:
# # Example script for testing Qs # TARGET R-FACTOR CYCLES 1 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
Once all these files are created and are in a single directory, the Qs job can be launched onto the cluster.
Here is a sample qsub script (named Qs.qsub):
#!/bin/bash #PBS -N Qs_test #PBS -e Qs_test.err #PBS -o Qs_test.log cd $PBS_O_WORKDIR /usr/local/bin/Qs Qs_test.in > Qs_test.log
The Qs.qsub script can be submitted to the cluster with the command
$ qsub -l nodes=1 Qs.qsub
Parallel use
Typically, a search is done with multiple cycles of minimization. These cycles can be broken into seperate jobs and run on individual processors to save time and utilize the power of the cluster. Create a series of subdirectories corresponding to each run (for example mod_1, mod_2, mod_3, etc.), copying the files needed to run into each. Set the CYCLES parameter to 1. Set the SEED parameter is different for each input file, otherwise the minimzations will all be identical. Then either submit each with single qsub scripts, or with the swarm command.
Here is an example swarm file (named Qs.swarm):
cd /data/user/mod_1; /usr/local/bin/Qs test_1.in > test_1.log cd /data/user/mod_2; /usr/local/bin/Qs test_2.in > test_2.log cd /data/user/mod_3; /usr/local/bin/Qs test_3.in > test_3.log cd /data/user/mod_4; /usr/local/bin/Qs test_4.in > test_4.log cd /data/user/mod_5; /usr/local/bin/Qs test_5.in > test_5.log cd /data/user/mod_6; /usr/local/bin/Qs test_6.in > test_6.log cd /data/user/mod_7; /usr/local/bin/Qs test_7.in > test_7.log cd /data/user/mod_8; /usr/local/bin/Qs test_8.in > test_8.log
The Qs.swarm script can be submitted to the cluster with the command
$ swarm -l nodes=1 -f Qs.swarm
Output
Aside from the redirected output file, a series of PDB files containing the final coordinates of your search model(s) from each minimisation is generated.
The program will also create a PDB file containing the coordinates of all symmetry equivalent copies of all search models, which can be viewed directly with RasMol (to check for bad contacts). You will need an X11 connection to run RasMol. Type rasmol QsXXX_packing.pdb and then type set unitcell on followed by set stereo on, colour chain, and backbone. You should now have a coloured side-by-side stereo image of the contents of 2x2x2 unit cells corresponding to the XXXth minimisation.
Additionally, a series of postscript files are generated. The files are colour postscript files containing projections of the model unit cell and central sections through the molecular transform(s), and are completely useless from the structure determination point of view (see keyword POSTSCRIPT for more information). Viewing postscript files - requires an X11 connection, gs myfile.ps. Type man gs for more information.
More information and finer details
Qs is pretty straightforward to use, but like ice hockey and bubble gum, it also takes time to master the finer details. For those who want more information see the Qs Online Help.
Warnings
Qs is ultimately dependent on physical memory to work well. Large unit cells and high resolution data require a great deal of memory. If your job fails to progress (as seen by either no output, or output stopped at some point), the node may be caught in a continuous swap cycle. Memory usage of a node can be seen in the live biowulf monitor. This may result in the node hanging, and your job will not complete. If this is the case, stop the job and resubmit with a lower resolution range.