[phenixbb] Phaser, Phenix and Em models

Randy Read rjr27 at cam.ac.uk
Mon May 11 01:24:30 PDT 2009


As it happens, we've been working very hard over the last few months  
first to make all commands in Phaser available from Python (done) and  
second to make all options available from the new Phenix GUI  (getting  
close).  ("We" in this context mostly means Airlie at our end and Nat  
at the Berkeley end.)  So it should become easy to switch to using  
density instead of coordinates for your models without switching to  
the command-line mode of running Phaser.  We're also very interested  
in optimizing the way that we use density from EM, which is something  
we haven't spent enough time playing with yet.  It's not yet possible  
to use density for a model in the MR-SAD mode--that's been on the wish  
list and shouldn't be too hard.  Do you need that feature right now?

I really like your other ideas, so we'll have to talk to Tom about  
adapting the AutoMR wizard so that it doesn't require a coordinate  
file.  As you say, this will be a real growth area!

All the best,


On 8 May 2009, at 15:39, Gino Cingolani wrote:

> Hi Randy,
> what about implementing the use of EM-models (e.g. structure factors
> from EM model) in Phenix to carry out MR and/or MR-SAD?
> There's a growing number of macromolecular complexes that have been  
> imaged
> at medium/low res by EM, which could be of great help to
> phase at low res or located anomalous scatterers in phased maps.
> And the EM database keeps growing!
> At this moment, it is certainly possible to use EM models in Phaser,
> but the Phenix pipeline could add much more to that. For instance,
> Phenix would allow for better phase extension of low res EM phases  
> to higher
> res by ncs-averaging or multi-crystal averaging (in Resolve).
> Or Phenix could help combining low res EM phases with other phase
> sources such as SeMet sites, poorly occupied heavy atom sites, etc  
> (MR-SAD).
> Or Phenix could rigid body refine (at low resolution) pseudo-atomic  
> models
> obtained by filling in EM-models with dummy atoms.
> This would help defining averaging masks and so on.
> What do you think?
> Thanks in advance,
> Gino
> ***********************************************************
> Gino Cingolani, Ph.D.
> Assistant Professor
> Dept. of Biochemistry and Molecular Biology
> SUNY Upstate Medical University
> 750 E. Adams Street, Syracuse, NY, 13210
> Tel.   (315) 464 8744
> Fax.  (315) 464 8750
> Email:  cingolag at upstate.edu
> ***********************************************************
> "Nati non foste per viver come bruti,  ma per seguir virtute e  
> conoscenza"
> ("You were not born to live like brutes, but to follow virtue and
> knowledge")
> Dante, The Divine Comedy (Inferno,  XXVI, vv. 119-120)
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

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- 

More information about the phenixbb mailing list