[phenixbb] 'Tasks' tab missing from 1.3b GUI and HL coefficients from a model

Stephen Graham stepheng at strubi.ox.ac.uk
Thu Jun 21 03:21:33 PDT 2007

Hi Peter,

> I think that the missing 'task' tab is a feature. Look under 'projects'
> -> 'preferences' to have the task window displayed.

Thanks for that.  Yes, now I can see my 'Tasks' tab (perhaps the
tutorial at http://www.phenix-online.org/download/documentation/phenix/prerelease/introduction/i00.html
could be updated to reflect the fact that 'Tasks' are hidden by

Unfortunately, however, I was still unable to work out how I can use
phenix to generate phases and FOMs from a PDB model (from simulated
annealing in phenix.refine) for use in the prime-and-switch strategy.
The map_coeffs.mtz from phenix.refine does not seem to have all of the
requisite columns...  Is there a 'phenix' way to do this, or should I
just use SFALL?

Also, while we are talking about map_coeffs.mtz, is there a
command-line flag to turn off the automatic map generation by
phenix.refine?  I use coot to generate my maps from map_coeffs.mtz on
the fly, so I would prefer not to have phenix.refine make maps for me.

And one last question, just for fun.  Can phenix.refine handle 'hard'
(constrained, strict) NCS?  I am working at low res with 4 molecules
per ASU and would prefer to just have one chain modelled plus an NCS
matrix to generate the other chains.  However, all the documentation I
have read leads me to believe that only 'soft' (restrained) NCS is
possible at the moment.  Is this the case?

Thanks again,


Dr Stephen Graham
Nuffield Medical Fellow
Division of Structural Biology
Wellcome Trust Centre for Human Genetics
Roosevelt Drive
Oxford OX3 7BN
United Kingdom
Phone: +44 1865 287 549

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