[phenixbb] MRage run
gb360 at cam.ac.uk
Mon Mar 17 05:06:51 PDT 2014
you should limit the number of sculptor protocols you use (default: all,
i.e. 13). When MRage processes your HHPRED search, it will convert each
template structure to 13 models, and this is quite many (this seemed
like a good idea when I played with this initially, but with more
experience, I would possibly change the limit to one protocol or a
selection of the most diverse protocols).
The keyword for this is "sculptor_protocols" (for some reason, I do not
see it in the GUI, but I will make sure it shows up in the next
version), and you can just set it to the protocols you want; protocol 1
is the sculptor default, and there is a keyword "minimal" for the 3 most
As for what MRage is doing, this should be in the logfile (this is also
available from the GUI). Just search for "Summary of searches", and you
get a table for each one-model extension. The logfile is indeed a bit
too verbose right now, and we are thinking of ways of making it more
readable (or more representable through the GUI).
On 2014-03-17 03:33, Jobichen Chacko wrote:
> Dear All,
> I am running a molecular replacement using MRage program for almost 1
> week with 4 threads, but yet to finish the run. I am using Phenix
> Version dev-1549
> I am having a pretty big protein (around 100 KDa).
> I gave data file, sequence file, one model pdb and output from HHpred
> as input.
> Is there anyway to to find out when it is going to finish the run, or
> I can extract any information from the current run, if I manually
> end the run?
> Thank you.
> phenixbb mailing list
> phenixbb at phenix-online.org
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