[phenixbb] Phaser, Phenix and Em models

Tom Terwilliger terwilliger at lanl.gov
Mon May 11 08:35:55 PDT 2009

Hi Gino,

I think that we should be able to modify the AutoMR wizard to take  
density maps instead of models.  I'll work with Randy and Airlie and  
Nat to do this.

-Tom T

Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

On May 11, 2009, at 2:24 AM, Randy Read wrote:

> Hi,
> 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,
> Randy
> 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)
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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: rjr27 at cam.ac.uk
> Cambridge CB2 0XY, U.K.                       www-
> structmed.cimr.cam.ac.uk
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