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Hi,
I'm running a molrep job on a protein with approx ~4500 atoms and ~550
residues using the adv (slow) search algorithm and the log file shows
that 31h 44m 43s remains.
1) Is that an accurate estimate?
2) Using the same algorithm on the same machine but using ccp4-4.2.2,
this search took ~3.25 hours. What is the difference in the algorithm or
default setting that causes such a difference in total processing time?
Is it the # of cycles of rigid body refinements before and after
translational search? I think the default in 5.99.5 is 10 after search,
what was it in 4.2.2?
3) Is it possible to parallelize (e.g. using data decomposition ) the
molrep algorithm or at least make an option for running N number of
threads for people with SMP systems or SSI (single system image) clusters?
VIRT RES SHR S %CPU %MEM TIME+ COMMAND
209m 50m 2532 R 99.9 1.4 1296:24 molrep
..and still going..
Thanks,
Sabuj Pattanayek
