[phenixbb] MRage run
Gabor Bunkoczi
gb360 at cam.ac.uk
Mon Mar 17 05:06:51 PDT 2014
Hi Jobi,
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
diverse ones.
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).
BW, Gabor
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.
>
> Jobi
>
>
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