[phenixbb] automr wizard: searching for all plausible space groups option

Randy Read rjr27 at cam.ac.uk
Thu Dec 8 07:26:00 PST 2011

In addition to Nat's suggestion about using a newer version, it's possible that AutoMR is confused by setting all_plausible_sg_list to an invalid value.  It should be a list of space groups to test, so True is not a legal value and I suspect a list has to be enclosed in quotes.  It should work if you just say


without giving any list.

I'm not sure why setting space_group didn't work, unless 1.6.1 predates the change of variable name from sg to space_group.



On 8 Dec 2011, at 05:05, Vitali Stanevich wrote:

> Hi,
> I'm trying to solve structure by MR with phenix 1.6.1-357 version. I have 100% identity search model and can find solution without problem in ccp4i in P212121 sg. But, I can't do it in phenix.automr command line because program looks only for P222 space group (pointed out by Randy Read). I use .sca from hkl2000 and running program from parameters file. I tried:
> ...
> all_plausible_sg_list = True
> use_all_plausible_sg = True
> ...
> all_plausible_sg_list = P222 P2221 P21212 P212121
> use_all_plausible_sg = True
> ...
> space_group = "P 21 21 21"
> ...
> They lead to report that no solution found or program being stalled (last variant). What should I do to make phaser search for all space groups in P222 point group?
> Thanks,
> Vitali 
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Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research      Tel: + 44 1223 336500
Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
Hills Road                                    E-mail: rjr27 at cam.ac.uk
Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk

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