[phenixbb] calculate map from ensemble refinement

Bard, Joel Joel.Bard at pfizer.com
Tue Jul 23 13:41:51 PDT 2013

I tried phenix.maps again on a machine with more memory and it seems to work.  On my workstation (8GB) it eats 100% of memory and then 100% of swap and then dies.  I'd still be curious to get the official ensemble refinement map scripts to see if the result is the same but the phenix.maps map looks very reasonable.



From: Pavel Afonine [mailto:pafonine at lbl.gov]
Sent: Tuesday, July 23, 2013 3:16 PM
To: PHENIX user mailing list
Cc: Tom Burnley; Bard, Joel
Subject: Re: [phenixbb] calculate map from ensemble refinement

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) models..


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.



On 23 July 2013 17:05, Bard, Joel <Joel.Bard at pfizer.com<mailto:Joel.Bard at pfizer.com>> wrote:

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.



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