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Phenix: Difference between revisions
→phenix.autosol - experimental phasing "wizard"
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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 == | ||