[phenixbb] error in Phaser

Randy Read rjr27 at cam.ac.uk
Thu Mar 14 06:59:52 PDT 2019

Dear Alexandra,

I have a suspicion that this has to do with a problem in specifying the molecular weight of your search model.  With electron density, Phaser can’t count up atoms and work out the molecular weight for itself.  In your job, you said protein was 0.9 and nucleic acid was 0.1, but Phaser interprets those numbers as molecular weight in Daltons!  So when it was looking at the map to figure out what to flag as occupied volume for a packing test, there wasn’t enough content to fill significant volume.  Try giving the right numbers in setting up the map ensemble, and let me know if you’re still having trouble!

Best wishes,

Randy Read

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 13 Mar 2019, at 13:41, Alexandra Deaconescu <alexandra_deaconescu at brown.edu> wrote:
> Hello,
> I have been trying to run Phaser using a map ensemble when I encountered the error listed below, which caused Phaser to fail. I have also attached the log file. Any help would be much appreciated.
> Thank you,
> Alexandra
> UNHANDLED ERROR: Program internal error in source file TraceMol.cc (line 229)
> *** Consistency check (wang_mask.size()) failed. ***
> <pAD6DNA_phaser.log>_______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
> Unsubscribe: phenixbb-leave at phenix-online.org

More information about the phenixbb mailing list