Phenix: Difference between revisions

2,587 bytes added ,  1 May 2011
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=== [http://www.phenix-online.org/documentation/autosol.htm phenix.autosol] - experimental phasing "wizard" ===
=== [http://www.phenix-online.org/documentation/autosol.htm phenix.autosol] - experimental phasing "wizard" ===


phenix.autosol uses HYSS, SOLVE, Phaser, RESOLVE, xtriage and phenix.refine to solve a structure and generate experimental phases with the MAD, MIR, SIR, or SAD methods  
phenix.autosol uses HYSS, SOLVE, Phaser, RESOLVE, xtriage and phenix.refine to solve a structure and generate experimental phases with the MAD, MIR, SIR, or SAD methods
 
=== [http://www.phenix-online.org/documentation/phaser_ep.htm phenix.phaser] - SAD phasing with Phaser ===
 
[http://www.phaser.cimr.cam.ac.uk/index.php/Phaser_Crystallographic_Software Phaser] can do SAD phasing - it is therefore called phaser_ep (ep stands for "experimental phasing"). The most recent version of Phaser is 2.3 in Phenix, and 2.1 in CCP4. Please note that the "Phaser" link of [http://www.phenix-online.org/documentation/phaser_ep.htm] in the sentence "consult the documentation for AutoSol or Phaser, or the Phaser WIKI"  points to the 2.1 documentation. The keywords are concisely (but somewhat lightly) documented at [http://www.phaser.cimr.cam.ac.uk/index.php/Keywords]. A script documenting the following features
# using a PDB file (with origin-centered coordinates) as a heavy atom cluster template
# using two different substructure atomtypes (the cluster, and Fe)
# using a PDB file of a preliminary protein model, for finding sites
# using a MTZ file of a preliminary protein model, for finding sites
# using known sites (from e.g. SHELXD or HYSS)
# 3. and 5. are combined in this example
is shown below:
<pre>
phenix.phaser <<eof
CTITLe XXX W12 SAD
MODE EP_AUTO
 
# name for output files:
ROOT XXXphaser
 
COMPOSITION PROTEIN NRES 2000 NUMBER 1
WAVELENGTH 1.2029
RESOLUTION 70 4.5
# HAND BOTH
 
# file with F+ F- SIGF+ SIGF- from XDS/XDSCONV using filetype CCP4_F:
HKLIN XXXp.mtz
CRYSTAL unknown DATASET unknown &
        LABIN Fpos = F(+) SIGFpos = SIGF(+) Fneg = F(-) SIGFneg = SIGF(-)
 
# use a rough model of the protein to get phases:
PARTIAL PDB    rigid.1.pdb RMS 2.
# alternatively a MTZ file can be used, but the PDB should be preferred
# PARTIAL HKLIN  rigid.1.mtz RMS 2.
 
# if sites are known, use them:
ATOM CRYSTAL unknown PDB knownsites.pdb
# the next keywords are documented at http://www.phaser.cimr.cam.ac.uk/index.php/Keywords
# here they are commented out since the file knownsites.pdb is from an earlier phaser job.
# ATOM CHANGE BFACTOR WILSON ON
# ATOM CHANGE SCATTERER XX
# BFACTOR WILSON RESTRAINT OFF
 
# the W12 cluster was found in Hicup (xray.bmc.uu.se/hicup/) and put at the origin
# using moleman2's "xyz cen" command (I don't know if this is necessary!)
CLUSTER PDB keg-cen.pdb
# the scatterer XX is predefined and refers to the cluster! Where is this documented ??
# FP and FDP are just guesses; fortunately FDP is refined
# however it is not documented what F0 of the cluster is!
SCATTERING TYPE XX FP=-1 FDP=13 FIX OFF
 
LLGCOMPLETE NCYC 50
LLGCOMPLETE COMPLETE ON
 
LLGCOMPLETE SCATTERER XX
LLGCOMPLETE SCATTERER Fe
 
eof
</pre>


== Molecular replacement ==
== Molecular replacement ==
1,330

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