[phenixbb] Troublesome molecular replacement

Randy Read rjr27 at cam.ac.uk
Mon Oct 29 14:52:08 PDT 2012


Even the latest version of Phaser may not have accounted for the translational NCS in this case.  If you have a peak at 0,0,1/4, then you likely have another one at 0,0,1/2 and (though it's not independent) there will be one at 0,0,3/4.  If there is more than one unique Patterson peak above the default of 20% of the origin, Phaser currently decides not to use it, because the current treatment is not optimized for more than one translation operator.

However, if you do have peaks at 0,0,1/4 and 0,0,1/2, then you can tell Phaser that there is 4-fold translational NCS, in which case it will expect to find 4 molecules in a row.  Unfortunately, I discovered a small bug in the Phenix GUI and, in the 1.8.1 release, if you try to change Phaser's behaviour, the commands aren't currently passed on to the program.  So, for the moment, you would be best running the job from a command script, adding the following two commands:

TNCS PATT PERCENT x (where x is a number between the top two Patterson peak heights)

This will be fixed reasonably soon, but I think there are other bugs right now...


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

On 29 Oct 2012, at 21:02, Yuri wrote:

> Nat,
> Just a few simple thoughts:
> --1) Are you certain about the space group, and did you try letting
> --Phaser pick one for you?  (It sounds like you did, but I can't tell
> --from your description.)
> I searched for a solution in all possible space groups in P 4. I thought I was certain of the space group, but maybe not...
> --2) How much refinement did you run to get an R-free of 42$, and did
> --you already try running AutoBuild with rebuild-in-place turned off?
> --Refinement alone may not have the radius of convergence you need.
>  True, I only did a couple of rounds of rebuild/refine
> --3) What is the sequence identity?
> My model is a point-mutant of the crystal.
> --4) Are you using the latest version of Phenix?  Phaser has had TNCS
> --support for almost a year now but I keep hearing from people who are
> --using ancient versions...
> I am using the latest official PHENIX built.
> ---
> -- 
> Yuri Pompeu
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