[phenixbb] calculate map from ensemble refinement

Pavel Afonine pafonine at lbl.gov
Tue Jul 23 12:15:37 PDT 2013

Hi Joel,

phenix.maps actually supposed to handle multi-model files provided that 
the occupancies are meaningful (equal to 1/N, where N is the number of 
models). But honestly I've never tried it with more than a few (5-10) 


On 7/23/13 8:20 AM, Tom Burnley wrote:
> Hi Joel,
> Short answer is no you need to run the jobs again.  However if they 
> took an age to complete let me know as I have some scripts that can 
> help reconstruct the maps.  Also please could you email me (off list) 
> the input parameter file you used.  You are correct that the 
> map_type=None likely caused the crash but I'd like to check that and 
> make it so it intercepts this issue earlier in the code.
> Cheers,
> Tom
> On 23 July 2013 17:05, Bard, Joel <Joel.Bard at pfizer.com 
> <mailto:Joel.Bard at pfizer.com>> wrote:
>     Hi-
>     I ran phenix.ensemble refinement which worked very nicely but
>     crashed during map output.  I think this was my fault for using a
>     parameter file that had map_type = None (I didn't look and assumed
>     the default was reasonable).  I would like to calculate maps after
>     the fact.  Is there a way to run the map calculation on the output
>     ensemble pdb file and reflection data?  I tried phenix.maps which
>     choked on the huge ensemble.
>     Thanks,
>     Joel

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