Hi Randy,
thanks for getting back to my email.
Yes, I do think it would be very helpful to switch to using
density instead of coordinates both for MR and MR-SAD.
The interface between cryo-EM and X-ray is growing so fast that in
many cases EM densities could be used for initial phasing by Fourier
difference, or even ab initio, provided sufficient ncs is available.
In our specific case we have at least two macromolecular complexes
(1.1-2.2MDa)
with >400SeMet, resolutions in the mid 3A with extreme unisomorphism and
10-15A EM densities.
SAD/MAD phasing is unrealistic, MIR methods can't work when all crystals are
inherently unisomorphic
.... MR/MR-SAD could be an alternative.
Thanks again!
Gino
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)
> _______________________________________________
> 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-
structmed.cimr.cam.ac.uk
_______________________________________________
phenixbb mailing list
phenixbb at phenix-online.org
http://www.phenix-online.org/mailman/listinfo/phenixbb
***********************************************************
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)