A Script for Automated Experimental Phasing Using Shelx C/D/E A Script for Automated Experimental Phasing Using Shelx C/D/EGeneral description - GUI - Presentations - Download - Help - Examples - Dependencies - References
SHELIXIR is a simple command-line tool with minimal software dependencies for a wide analysis of phasing information using the SHELX C/D/E software package. The script was written for quick and blind analysis of synchrotron datasets on site.
The script novelty is in:
SHELIXIR has own graphical user interface - SHELIXIR_GUI.
Talk about SHELIXIR: PDF
Tutorial with GUI: https://youtu.be/CZIziPv28hA
Command-line tutorial: https://youtu.be/dqi5_yLhWOc
Actual stable version of SHELIXIR (2.1) is to be downloaded here. To install SHELIXIR, simply download the file, make it executable (e.g. using "chmod +x") and put it to the system path.
Older versions of (ba)SHELiXir:
Usage: shelixir [params...]
Params:
-prefix foo Sets prefix as foo
-output-dir path Sets output directory (must be created before)
-sad foo.hkl Sets foo.hkl as a SAD dataset
-nat foo.hkl Sets foo.hkl as a native dataset
-peak foo.hkl Sets foo.hkl as a peak dataset
-infl foo.hkl Sets foo.hkl as an inflection dataset
-hrem foo.hkl Sets foo.hkl as a high remote dataset
-lrem foo.hkl Sets foo.hkl as a low remote dataset
-before foo.hkl Sets 'native' dataset for RIP phasing
-after foo.hkl Sets dataset collected after the radiation damage
-sira foo.hkl Sets SIRAS dataset
-seq foo.seq Sets sequence file in FASTA format
-nproc N Sets N parallel processes in ShelxE routine
-sfac X Sets heavy element
-find N Sets number of searched atoms
-ntry N Sets number of trials to search for substructure
--cell [a] [b] [c] ... Sets unit cell parameters: unit cell dimensions
... [alpha] [beta] [gamma] ... and angles
-wavelength X Sets wavelength in Angstroms
-res X Y Sets the low and the high resolution for phasing
-dsul N Sets number disufides at lower resolution
-mind "X Y" Sets the parameters for MIND
-dsca X Sets the DSCA parameter for RIP or RIPAS
-Epar "par1 par2 ..." Sets the ShelxE parameters (DO NOT FORGET ""!)
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SCREENING AND PARALLELIZATION PARAMETERS
-bravais xX Sets the Bravais-type (e.g. tP)
-list "SG1 SG2 ..." Sets list of space groups to be examined
-solv x X s Sets the minimal, maximal and with fraction steps
(e.g. -solv 27 81 2)
-solv_auto Screens the sol. cont. from 20% to 80% with 5% step width
-fix_low X Sets the low resolution for the high-resolution screening
-screen_high "X Y Z ..." Sets the high resolution limits for screening
-fix_high X Sets the high resolution for the low-resolution screening
-screen_low "X Y Z ..." Sets the low resolution limits for screening
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Most frequent ShelxE parameters:
-h heavy atoms are included in the native structure
-hN when the nummber N of heavy atoms is known
-aN runs N cycles of auto-tracing
-q explicit search for helices
-s[x] sets fraction of solvent content (e.g. -s0.45)
-e runs free lunch algorithm (e.g. -e1.2)
-z optimizes the heavy atom substructure before the density modif.
-mN N iterations of density modification per global cycle (e.g. -m5)
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Bravais-types (according to the XDS notation):
aP: P1
mP: P2, P21
mC: C2
oP: P222, P2221, P21212, P212121
oC: C222, C2221
oF: F222
oI: I222, I212121
tP: P4, P41, P42, P43, P422, P4212, P4122, P41212, P4222, P42212, P4322, P43212
tI: I4, I41, I422, I4122
hP: P3, P31, P32, P312, P321, P3112, P3121, P3212, P3221,
P6, P61, P65, P62, P64, P63, P622, P6122, P6522, P6222, P6422, P6322
hR: R3, R32
cP: P23, P213, P432, P4232, P4332, P4132
cF: F23, F432, F4132
cI: I23, I213, I432, I4132
Alternative:
-list "SG1 SG2 ..." sets list of space groups to be used in automated phasing
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Viscotoxin-A1 is distributed as an easy SAD tutorial with Shelx C/D/E.
Fibronectin is distributed as a difficult SAD tutorial with Shelx C/D/E.
Elastase is another tutorial for Shelx C/D/E.
P9 is Phenix tutorial. (link)
Original data that lead to phasing of olive flounder interferon gamma (PDB id 6F1E).
GerE is MAD tutorial for Shelx C/D/E.
P. Kolenko, J. Stransky, T. Koval, M. Maly, J. Dohnalek. (2021). SHELIXIR: automation of experimental phasing procedures using SHELXC/D/E. J. Appl. Cryst., 54, 996-1005.
P. Kolenko (2019), baSHELiXir: A Bash Script for Automated Experimental Phasing Using Shelx C/D/E. Chemicke listy, 113, 610-614.
I. Uson & G.M. Sheldrick (2018), "An introduction to experimental phasing of macromolecules illustrated by SHELX; new autotracing features" Acta Cryst. D74, 106-116 (Open Access) if SHELXE proves useful.