[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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