Dear Paul,
this is very interesting! From the list of changes, it appears that in
version 1.6.1, you use a similar idea to implement hydrogen bonds via
DSSP during refinement that I used to stabilize the 4.3 A refinement of
Pol II in complex with TFIIB [1]:
CHANGE LOG for PHENIX distribution
==================================
Version 1.6.1
=============
<snip>
- phenix.refine
- much faster rotamer fixing
- initial implementation of secondary structure restraints (hydrogen
bonds)
- automatic assignment of sec. str. using KSDSSP (from UCSF CGL)
- proper treatment of charges on metal ions for scattering factors
</snip>
Could you please give more details of how this is implemented? What are
your hydrogen bond target distances and sigmas? Do you update this list
during refinement?
I used a simple list of additional 2.9 A target-"bond"-distances between
N and O with a target sigma of 0.05 A. This list was determined with
DSSP and a self-made Fortran95 program using a user-defined
"energy-threshold" prior to refinement and was kept constant during
refinement.
Personally, I think, using secondary structure hydrogen bonds should be
an option in every refinement program, especially at lower resolution!!!
The BUSTER Wiki describes the procedure that I used. For REFMAC, I
haven't seen anything similar, yet.
Very exciting!
Best regards,
Dirk.
[1] Nature 462, 323-330, (2009)
Am 31.03.10 04:41, schrieb Paul Adams:
> The Phenix developers are pleased to announce that version 1.6.1 of
> Phenix is now available. Binary installers for Linux, and Mac OSX
> platforms are available at the download site:
>
> http://phenix-online.org/download/
>
> Just some of the new features in this version (1.6.1) are:
>
> - Fast automated rotamer fixing in phenix.refine
> - Use of atomic charge in calculation of scattering factors
> - New Graphical User Interfaces for phenix.superpose_pdbs,
> phenix.get_cc_mtz_mtz,
> phenix.get_cc_mtz_pdb, and phenix.fmodel
> - Consolidated validation tool in GUI
> - New map calculation tool, phenix.maps (also used in GUI)
> - Rapid loading of structures in GUI selection editor
> - Improved geometry restraints to maintain amino acid rotameric states
> - Alpha version of secondary structure restraints
> - Automated secondary structure analysis with KSDSSP (code from UCSF CGL)
>
> For a full list of changes see:
>
> http://www.phenix-online.org/documentation/CHANGES
>
> Please note that there is a new publication that should be used to
> cite use of Phenix:
>
> PHENIX: a comprehensive Python-based system for macromolecular
> structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B.
> Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral,
> R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J.
> Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H.
> Zwart. Acta Cryst. D66, 213-221 (2010).
>
> Full documentation is available here:
>
> http://www.phenix-online.org/documentation/
>
> There is a Phenix bulletin board:
>
> http://www.phenix-online.org/mailman/listinfo/phenixbb/
>
> Please consult the installer README file or online documentation for
> installation instructions.
>
> Direct questions and problem reports to the bulletin board or:
>
> [log in to unmask] and [log in to unmask]
>
> Commercial users interested in obtaining access to Phenix should visit
> the
> Phenix website for information about the Phenix Industrial Consortium.
>
> The development of Phenix is principally funded by the National
> Institute of
> General Medical Sciences (NIH) under grant P01-GM063210. We also
> acknowledge
> the generous support of the members of the Phenix Industrial Consortium.
>
--
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Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
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Germany
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