Small Angle X-ray & Neutron Scattering Group (SAXNS)


Small Angle X-ray & Neutron Scattering Group (SAXNS)

This group of Structural Biologists from several Gulf Coast Consortia instituions has joined together to promote biological SAXS (BioSAXS) in the Greater Houston Area. We have recognized the need to supplement our crystallographic, NMR, electron microscopy, and biochemical data, with solution scattering. Our research interests cover a broad area, but need additional information about our systems, such as: conformational rearangement, protein:protein or protein:nucleic acid interactions, and the conformational ensemble of states, that can most readily be determined via solution scattering.

Founding Members

  • Mark A. White,
  • Woldek Bujalowski
  • Kay Choi
  • James C. Lee
  • Marc C. Morais
  • A. Oberhauser

  • Lawrence Sowers
  • Jianpeng Ma (BCM)
  • Qinghua Wang (BCM)
  • Francis Tsai (BCM/Rice)
  • Edward Nikonwicz (Rice)

  • Robert O. Fox (UH)
  • John Ladbury (MD Anderson)
  • John McMurray (MD Anderson)
  • Stan Watowich
  • Xiaodong Cheng

EVENTS


SAXS Instrumentation

Rigaku BioSAXS-1000

The Rigaku BioSAXS-1000 coupled with the FR-E++ x-ray source provides the best home-lab SAXS camera for biological samples. The camera is equiped with a 96-well automatic sample changer (ASC-96) with an in-vacu quartz flow-cell. In addition, we have several quartz sample cells for manual loading of smaller sample volumes or detergent samples, which are not compatible with the ASC-96 liquid handling system. The quality of SAXS data obtained with the BioSAXS camera has been exceptional. Using our in-house SAXNS web-services for data processing and analysis the optimal quality data can be collected. It is not unusual to collect useful data to the limit of the detector (q~0.7 Å-1). The SCSB BioSAXS facility fulfills a regional need for BioSAXS instrumentation and expertise.

Documents for the BioSAXS-1000


The SCSB BioSAXS Facility

The SCSB research resources consist of several Center research labs designed to pursue intensive use of instrumentation by UTMB Structural Biologists, and thus are considered research facilities rather than fee-for-service cores. This includes the MXL BioSAXS facility. Facility users must supply their own materials and personnel associated with the measurement, otherwise there are no fees for users. In almost all cases, use of Center research resources is initiated either by a full member of the Center faculty or a Center Facility Lab Manager. Full Center faculty members (PIs) are entitled to engage in research of their own or in collaboration. There have been several regional BioSAXS collaborations between the SCSB and Texas area researchers. However, before initiating a project ALL researchers must: (1) Discuss the project with a Center collaborator and (2) Sign a memorandum of understanding (MOU) for the project. The MOU outlines the role of Center and researcher. The MOU is usually created by the Manager for the collaborator.

To initiate a project in the Center please contact:
A Center Faculty member,
the Facility Manager (Mark Andrew White, Ph.D.),
Or the Center Director, Monte Pettitt,Ph.D.


University BioSAXS Instruments

North America

  • U. Wisconsin NMRFAM (NanoStar)
  • U. Pennsivania PSM* (P-SAXS)
  • U. Tennesee Knoxville* (Xeuss)
  • U. Illinois MRL* (SAXS)
  • U. Chicago (GANESHA)
  • U. Massachusetts Amherst (GANESHA)
  • U. Texas MSI* (GANESHA)
  • Boston University MSE* (N8 Horizon)
  • Northwestern U. JBC* (SMAX-3000)

Small Angle X-ray or Neutron Scattering Beamlines

North America

The World

  • LNSL Brazil (SAXS)
  • Australian Synchrotron (SAXS)
  • Spring8 (BioSAXS)
  • World SANS Directory (SANS)

Software for Small Angle X-ray Scattering

  • ATSAS (Manuals) On-line - - -
  • PRIMUS (Manual) :Data Processing & GUI (WINDOWS)
    • PRIMUS will work on LINUX using WINE - Obsolete PRIMUS is now cross-platform
    • wineconsole /home/*****/.wine/drive_c/ATSAS/primus.exe
  • CRYSOL :crysol: Rigid body Fitting
  • GNOM :gnom: Rg Calculator
  • GASBOR :gasbori:gasborp:gasbormx: Molecular Envelope
  • DAMMIN :dammin: Random Atom Model
  • MONSA :monsa: "dammin" for protein/dna (non-uniform density) complexes
  • CORAL :coral: Combines SASREF+BUNCH
  • SASREF :sasref: Modelling of multisubunit complexes
  • BUNCH :pre_bunch:bunch: Rigid body Fitting
  • EOM :eom: Ensemble of Models
    • RANCH :ranch: Ensemble builder
    • GAJOE :gajoe: Ensemble Optimization
  • Command Line High-Throughput Automated Tools
    • DATCMP calculates the discrepancy between two data sets. Is used to check for radiation damage, to compare buffers.
    • DATAVER averages two or more data sets. Is used to average buffers, to average multiple sample exposures.
    • DATOP performs arithmetic operations. Is used to subtract buffer(s) from the sample, to scale against concentration.
    • DATCROP* crops the range of experimental data points.
    • DATREGRID* changes the grid of the given data.
    • ALMERGE* merges data collected from two different concentrations and extrapolates it to infinite dilution assuming moderate particle interactions.
    • AUTORG automatically computes Rg and I(0) using the Guinier approximation, estimates data quality, finds the beginning of the useful data range.
    • DATGNOM estimates Dmax, computes the distance distribution function p(r) and the regularized scattering curve.
    • DATPOROD computes Porod volume from the regularized scattering curve.
    • saxns_dammif gnom.out #Models {SYMM} {PDB}
    • saxns_dammifs gnom.out #Models {SYMM} {PDB}
    • saxns_gasbor gnom.out #Models {SYMM} {PDB}
    • saxns_bift saxs.dat -D/N/B/C {-smax=0.5} {-b -n # -e # -h}
    • saxns_model2pdbs 1pdb.pdb
    • saxns_clean4mes *.dat
    • saxns_jun2dat junXXX.int
    • saxns_crysol saxs.dat *.pdb
    • saxns_fit2eom *.fit
    • saxns_gavge #start #end {list of GA* run #s}
    • FOXS FoXS equivalent to CRYSOL
    • MES FoXS equivalent to EOM
  • Glatter & Kratky (SAXS Textbook) :(eds. O. Glatter & O. Kratky, 1982
  • MES (Manual) :mes DataFileList: Ensemble Optimization
  • Andrej Sali's Tools (UCSF)
    • IMP (Wiki)
      • FoXS - Compute SAXS profiles or fits from PDB files. (foxs)
      • Multi_FoXS - Ensemble analysis from PDBs or list of SAXS profiles. (multi_foxs)
      • FoXS_Dock - Docking program using multiple data type: CX,SAXS,NMR,EM. (idock)
    • Modeller (Docs, Wiki)
    • FoXS Fast SAXS Profile Computation with Debye Formula(Home page)
  • BioXTAS project
  • USAXS Jan Ilavksy
  • SASfit (Manual) :sasfit: Model fitting
  • SASTBX (Home)The Small Angle Scattering ToolBox / Web server (LBL)
  • SASTBX (Home)The Small Angle Scattering ToolBox / Web server (Canada)
  • SCATTER (Home) Forster/Apostol SAS software
  • SCÅTTER (Home) Ivan Rodic and Robert Rambo, SYBILS, SAS software
  • CCP13 (List) Software for SAS
  • SAXNS Utilities (Download v.2022-08-16)
  • SAXNS_DAMMIF : Uses the data in your gnom.out to generate {#} bead-models with symmetry {Symm}. These are then aligned and filtered. Optionally the filtered bead-model is aligned, and inverted as necessary, to a given {PDB}.
    • $SAXNS/saxns_dammif gnom.out {#} {Symm} {PDB} {oblate/prolate}
  • SAXNS_DAMMIFS : The SLOW version, uses up to 30,000 beads for when you have a large object!
    • $SAXNS/saxns_dammifs gnom.out {#} {Symm} {PDB} {oblate/prolate}
  • SAXNS_GASBOR :
    • $SAXNS/saxns_gasbor gnom.out {#aa} {#} {Symm} {oblate/prolate}
  • SAXNS_BIFT : Uses Steen Hansen's (https://somo.chem.utk.edu/bayesapp/) iftci program to determine the P(r)
    • $SAXNS/saxns_bift saxs.dat -D/N/B/C {-smax=0.5} {-b -n # -e # -h}
  • SAXNS_MODEL2PDBS : Extract individual MODELS from an NMR/MD PDB file
    • $SAXNS/saxns_model2pdbs 1pdb.pdb
  • SAXNS_CLEAN4MES : Prepare the FOXS output for use with MES
    • $SAXNS/saxns_clean4mes *.dat
  • EOM with a POOL : Use Crysol to get FIT files then make the inputs to GAJOE
    • SAXNS_CRYSOL : Run CRYSOL in batch model - multiple PDBs
      • $SAXNS/saxns_crysol saxs.dat *.pdb
    • SAXNS_FIT2EOM : Prepare junXYZ.int, RanchXYZ.log, Size_listXYZ.txt from crysol FIT files
      • $SAXNS/saxns_fit2eom *.fit
      • gajoe saxs.dat -i=junXYZ.int -s=Size_listXYZ.txt -r=RanchXYZ.log
  • SAXNS_JUN2DAT : Extract the scattering curves from an EOM junXXX.int
    • $SAXNS/saxns_jun2dat junXXX.int
  • SAXNS_GAVGE : Average and GNUPLOT several EOM distributions
    • $SAXNS/saxns_gavge #start #end {-h -r -d -c=# }
  • SAXNS_HELP : View the SAXNS README file
    • $SAXNS/saxns_help
  • Goldenberg-SAXS (Home) The U. Utah Goldenberg Lab's SAXS tools (python).
  • Fast-SAXS (Home) The Roux Lab's fast coarse-grained (CG) SAXS profiles computation program.
  • AXES (Home) SAXS PDB fitting using Explicit Solvent.
  • AquaSAXS (Home) Delarue Groups' SAXS PDB fitting with Solvent Mapping.
  • WAXSiS (Home) The WAXS in Solvent (MD) SAXS/WAXS PDB fitting server.
  • FlexFitSAXS (Home) The Zheng Lab's Elastic Network Model SAXS PDB fitting program.
  • Denfert (Home) The Koutsioubas/Pérez hydrated ab initio BEAD Model program.
  • DENSS (Home) The T.D. Grant ab initio Electron Demsity Mapping program. (Server)
  • SAXSTER (Home) SAXS Assisted Protein Folding.
  • Phaistos (Home) Protein Structure Prediction with SAXS and NMR restraints.
  • ENSEMBLE (Home) The Forman-Kay Lab's SAXS & NMR Ensemble fiting to PDB models.
  • WillItFit (Home) The Arleth Group's NanoDisk Fitting Routines: python $WillItFit/WillItFit.py
  • Memprot (Home) Coarse grain modeling of detergent corona around a membrane protein.

SAXS & SANS on the WEB

    SAS Data Repositories

  • SASBDB: Small Angle Scattering Biological Data Bank (EMBL)
  • BIOISIS: the resource for macromolecular SAXS. (SIBYLS)
  • wwPDB: ADIT-NMR currently supports NMR/SAXS depositions.

SAXNS UTILITIES

  • SAXNS Scripts (Download v.2022-08-16)
  • SAXNS_DAMMIF : Uses the data in your gnom.out to generate {#} bead-models with symmetry {Symm}. These are then aligned and filtered. Optionally the filtered bead-model is aligned, and inverted as necessary, to a given {PDB}.
    • $SAXNS/saxns_dammif gnom.out {#} {Symm} {PDB} {oblate/prolate}
  • SAXNS_DAMMIFS : The SLOW version, uses up to 30,000 beads for when you have a large object!
    • $SAXNS/saxns_dammifs gnom.out {#} {Symm} {PDB} {oblate/prolate}
  • SAXNS_GASBOR :
    • $SAXNS/saxns_gasbor gnom.out {#aa} {#} {Symm} {oblate/prolate}
  • SAXNS_BIFT : Uses Steen Hansen's (https://somo.chem.utk.edu/bayesapp/) iftci program to determine the P(r)
    • $SAXNS/saxns_bift saxs.dat -D/N/B/C {-smax=0.5} {-b -n # -e # -h}
  • SAXNS_MODEL2PDBS : Extract individual MODELS from an NMR/MD PDB file
    • $SAXNS/saxns_model2pdbs 1pdb.pdb
  • SAXNS_CLEAN4MES : Prepare the FOXS output for use with MES
    • $SAXNS/saxns_clean4mes *.dat
  • EOM with a POOL : Use Crysol to get FIT files then make the inputs to GAJOE
    • SAXNS_CRYSOL : Run CRYSOL in batch model - multiple PDBs
      • $SAXNS/saxns_crysol saxs.dat *.pdb
    • SAXNS_FIT2EOM : Prepare junXYZ.int, RanchXYZ.log, Size_listXYZ.txt from crysol FIT files
      • $SAXNS/saxns_fit2eom *.fit
      • gajoe saxs.dat -i=junXYZ.int -s=Size_listXYZ.txt -r=RanchXYZ.log
  • SAXNS_JUN2DAT : Extract the scattering curves from an EOM junXXX.int
    • $SAXNS/saxns_jun2dat junXXX.int
  • SAXNS_GAVGE : Average and GNUPLOT several EOM distributions
    • $SAXNS/saxns_gavge #start #end {-h -r -d -c=# }
  • SAXNS_HELP : View the SAXNS README file
    • $SAXNS/saxns_help

SAXNS WEB Services

  • SAXNS E-Subtr Estimates the buffer scale factor (absorption correction) & produces the sample scattering curve using the {Sample+Buffer} and {Buffer}. dat files. Output is calibrated so that Io = MW (Da). Runs AUTORG & DATGNOM, Rg and DMAX saved in Header, Subtracted and OUT files produced: (Recommended method of buffer subtraction for globular samples)
  • SAXNS P-Subtr Estimates the buffer scale factor (absorption correction) based on Porod's Law & produces the sample scattering curve using the {Sample+Buffer} and {Buffer} dat files from SAXSLab or any other 1-D data reduction package.( Experimental )
  • SAXNS CXS Determines the similarity of two scattering curves via the Chi2 metric. The two curves are scaled, with a zero-point offset and their differences, absolute and in sigma, are calculated. A Graphical plot is also produced. This is very usefull for determining if a dilution series has signicant differences between curves.
  • SAXNS Rambo Calculates the apparent Molecular Weight (MW) of the sample using the method of Rambo & Tainer (2013). This will accept and standard 3-column formatted SAXS data file (q, I, σ) with q in either $Aring;-1 or nm-1. Both AUTODAT and DATGNOM are used to calculate the RG and Io used in the calculation. A new DAT file is produced with the results of these calculations in the header, algong with the OUT file and data plots.
  • SAXNS PDDF This calculates the P(r) or Pair Distance Distribution Function (PDDF) for a given PDB structure file. The algorithm used is exceptionally fast as it uses a sparse sampling technique.( Alpha Version )
  • SAXSLab Scale Calculate the buffer scale factor (absorption correction) based on the transmission factors recorded in SAXSLab. Scale can be applied in either SAXSLab or PRIMUS. = USE SAXNS-ES =
  • SAXNS Re-bin This server will re-bin saxs data files by averaging in bins of fixed width (in Log(q)). The Guinier region data can be retained or re-binned. A maximum-q cutoff can also be applied, as well as a constant offset to correct issues with buffer subtraction.

SAXS UTILITIES

  • SAXS MoW Molecular Weight Calculator from LNLS Brazilian Synchrotron Light National Laboratory (SAXS MoW Server)
  • BayesApp SAXS P(r) iFT Calculator from Steen Hansen of the Niels Bohr Institute, Danmark.


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