[ccp4bb] Phenix version 1.6.4 released

[Paul Adams]

The Phenix developers are pleased to announce that version 1.6.4 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 (1.6.4) are:

- GUI:
  - new interfaces for eLBOW, CIF to MTZ conversion, phenix.find_ncs,  
phenix.superpose_maps
  - new structure comparison tool (evaluation of multiple related  
structures)

  - supports execution of jobs on the Sun Grid Engine queueing system
  - maps for PyMOL now output in (smaller, faster) CCP4 format
  - display of sequence and secondary structure in wizards and  
validation

  - new wide-format windows for wizards and phenix.refine
  - many bug fixes

- Automated model building:
  - phenix.autosol now much faster and improved model-building after  
density modification
  - phenix.phase_and_build (carries out an iterative process of  
building a model as
rapidly as possible and uses this model in density modification  
to improve the map.
Up to 10x faster compared to AutoBuild, but model quality is  
nearly as good)
  - phenix.build_one_model (quickly build a single model from a map  
and sequence file,

or extend an existing model)
  - phenix.assign_sequence (carry out an improved sequence assignment  
of a model that
you have already built. Uses the new loop libraries available in  
phenix.fit_loops)
  - phenix.apply_ncs (apply NCS operators to a single copy of a  
protein to create all

the NCS‐related copies)
  - phenix.find_ncs (now supports identification of NCS operators  
from a density map)
  - phenix.fit_loops (two main algorithms now available - fit short  
gaps using a loop
library derived from high‐resolution structures in the PDB, or  
build loops directly

by iterative extension with tripeptides

- phenix.refine:
  - reference model restraints (restraint dihedral angles to a higher  
resolution

reference model)
  - alternate ideal angles for torsion definitions (preserves side  
chain rotameric states)

  - automatic flipping of incorrect N/Q/H rotamers
  - custom planarity restraints
  - hydrogen-bond restraints for Watson-Crick base pairs
  - reflections with Fobs=0 used in refinement
  - automatic optimization of mask parameters
  - map parameters now consistent with phenix.maps
  - new custom_nonbonded_symmetry_exclusions atom selection parameter  
to fine tune

non-bonded interactions across symmetry axes

- Phasing:
  - Option for Phaser likelihood scoring of substructure solutions in  
HySS
  - SOLVE converted to C++; FORTRAN compiler no longer required for  
Phenix compilation


- Other:
  - KiNG kinemage viewer incorporated into Phenix
  - Real space refinement option in ligand fitting
  - B-factor sharpening option for maps

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.

--
Paul Adams
Deputy Division Director, Physical Biosciences Division, Lawrence  
Berkeley Lab

Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Head, Berkeley Center for Structural Biology

Building 64, Room 248
Tel: 1-510-486-4225, Fax: 1-510-486-5909
http://cci.lbl.gov/paul

Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 64R0121
Berkeley, CA 94720, USA.

Executive Assistant: Marian Harris [ mshar...@lbl.gov ] 
[ 1-510-486-6886 ]

--

[ccp4bb] non-isomorphism

[James Holton]

Does anyone have a good reference (beyond the original Crick  Magdoff 
work) for the magnitude of non-isomorphism typically observed in protein 
crystals?  For example, two crystals from the same drop usually yield 
scaled intensities that are within ~10% of each other, but cryo-cooling 
usually changes F by 10-20%.  At least, that has always been my 
impression, but now I find myself in need of a reference for this.  
Surely someone has done some kind of survey of R-iso between cryo and RT 
data sets?


-James Holton
MAD Scientist

[ccp4bb] problem running xtal_pdbsubmission.inp in CNS

[Sudhir Kumar]

Dear all
I have a problem regarding refinement in CNS
1. I had refined a structure in refmac5 with final R and Free R values
are 18.8 and 23.8 respectively. While running xtal_pdbsubmission.inp
on CNS, it shows the R and Free value of 24 and 24.4 in the output.
what could be the reason?
2. How to add the twinning information in CNS during the
refinement/generating PDB for deposition?
thanks in advance
-- 
best regards
Sudhir Kumar
Research Scholar
Structural Biology Laboratory
SLS, JNU,
New Delhi-110067

Re: [ccp4bb] Fab:Peptide complex crystallization

[Zhijie Li]

Fab:Peptide complex crystallizationHi Christine,

I never worked with Fab, but I do have a little experience with DMSO. 

I had a case in which I could grow my crystal in 10-15% DMSO - to use it as 
cryoprotectant. But in another case, 5% DMSO inhibited my crystal's growth. 
When I had DMSO as cryo, I found lots of pyramid shaped electron densities on 
my protein surface, which should be the DMSO molecules. These DMSO molecules 
sit in little indents on protein surface where the surrounding environments are 
relatively hydrophobic. My ligand (sugar) binding was not affected. 

I think DMSO is generally thought to weaken interactions, but not too much. For 
example, in PCR, DMSO is used for increasing the specificity of the primers, 
i.e., weakening the base pairing a little.

If you are going to add 1/10V of the 10% DMSO peptide solution to 1V protein, 
then the final DMSO concentration is only 1%. I do not think that will be too 
detrimental for the protein to crystallize, or for the peptide to bind. But 
beyond 5%, I would be cautious and will try gel filtering or dialyzing the 
mixture if the initial screen fails (but it may work!). 

Zhijie




From: Harman, Christine 
Sent: Monday, July 19, 2010 1:37 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Fab:Peptide complex crystallization


Hi all, 
I was wondering if anyone has had any experience with setting up Fab:peptide 
complexes for crystallization.  I have Fab protein and peptide and I am not 
sure how to add the peptide to the Fab protein.  My peptide is hydrophobic and 
thus not very soluble in standard aqueous buffers and barely soluble in some 
organics.  The Fab protein I have is currently in 100mM Sodium Acetate pH5, 
150mM NaCl.  My current plan is to dissolve lyophilized peptide first in 10% 
DMSO and use this stock to add to Fab protein in a 20:1 or 10:1 molar ratio.  I 
am not sure of the effects of residual DMSO on peptide binding to Fab or on 
crystallization.  I have read one paper in which they rave about DMSO as an 
additive in their crystallization, but that protein was not Fab like at all.  
Any insight you all might have on this would be greatly appreciated.

Thanks in advance, 

Christine 

[ccp4bb] Assistant Professor faculty position: Santa Cruz, CA

[William Scott]

Dear Colleagues:

If you know of anyone who might be interested in an assistant professor 
position, would you please be kind enough to bring the following advertisement 
to their attention?  

http://www.nature.com/naturejobs/science/jobs/154054-Assistant-Professor

Many thanks.

Bill Scott