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:
h...@phenix-online.org and b...@phenix-online.org
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.
--
*******************************************************
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone: +49-89-2180-76845
Fax: +49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW: www.genzentrum.lmu.de
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