automr wizard: searching for all plausible space groups option
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
On Wed, Dec 7, 2011 at 9:05 PM, Vitali Stanevich
I'm trying to solve structure by MR with phenix 1.6.1-357 version.
Could you please try the latest version first? 1.6.1 is more than a year and a half old and there have been many changes in Phaser and AutoMR during that time. -Nat
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 use_all_plausible_sg=True 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. Regards, Randy 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: [email protected] Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
participants (3)
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Nathaniel Echols -
Randy Read -
Vitali Stanevich