Software Downloads

Below you will find crystallographic software developed by our Center members and Staff. This software was developed as part of the mission of the Sealy Center for Structural Biology and Molecular Biophysics X-ray Crystallography Laboratory. Our mission is to provide access to state of the art instrumentation, facilities, software, education and training for Center crystallographers.

PMB

Download PMB: GO

PMB is a a suite of programs and scripts for the refinement of crystallographic structures. The scripts use CNS for refinement and RESOLVE and CCP4 for some optional functions, such as NCS & density modification and maps for COOT. The package includes optional modified CNS modules, which improve the functionality of CNS. However, PMB is more than a wrapper for the CNS program. PMB includes several improvements for refining crystal structures, particularly in the case of low resolution data.

References

Singh R, White MA, Ramana KV, Petrash JM, Watowich SJ, Bhatnagar A, Srivastava SK., Structure of a glutathione conjugate bound to the active site of aldose reductase. Proteins: Structure, Function, and Bioinformatics 2006, July 1, 64(1), 101-110 {PDF}

Emily E. Scott, Mark A. White, You Ai He, Eric F. Johnson, C. David Stout, and James R. Halpert, Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9 A resolution: Insight into the range of P450 conformations and coordination of redox partner binding J. Biol. Chem 279, 26, 27294-301, 2004. {PDF}

IP Radial Calibration

Download Radial Calibration Utilities: GO

The MacScience DIP user can easily create and apply a new radial calibration. This technique offers a tool for recalibration of the DIP scanner, and a diagnostic for changes in detector sensitivity. This technique was developed prior to the new flood-field calibration applied to all new DIP scanners from 1996. The author believes that this technique offers the end-user a simpler more robust calibration and diagnostic tool than a flood field type calibration.

Reference

Mark A. White, Stanley J. Watowich, and Robert O. Fox, (1999), Calibration of Spiral Readout Image Plate Detectors, J. Appl. Cryst. 32, 65-70, 1999.(PDF)

Crystallographic Software Manuals

Data Processing

  • HKL (Manual) : hkl2000 : denzo : dip : xdisp :scalepack
  • CCP4 (Manual) (Type: ccp4_setup before using)
    • MOSFLM (Manual) : mosflm
    • POINTLESS (Manual) :
    • XTRIAGE (Manual) :mmtbx.xtriage
  • PROTEUM (Manual) (Windows Only for Bruker CCD)
  • XPRESS (Manual) (SGI Only for DIP2030)

Structure Solution

  • CNS (Manual) : cns
  • CCP4 (Manual) (Type: ccp4_setup before using)
  • SOLVE (Manual) : solve

Structure Refinement

  • CNS (Manual)
  • CCP4 (Manual) (Type: ccp4_setup before using)
  • SHELX (Manual)
  • RESOLVE (Manual) : resolve
  • PHENIX (Manual) :

Model Building

  • XtalView (Manual : How-to) : xtalmgr : xfit
  • COOT (Manual) (Type: ccp4_setup before using coot)
  • CCP4 (Manual) (Type: ccp4_setup before using)
  • O (Manual) : ono

Molecular Graphics

  • XtalView (Manual) : xtalmgr : xfit
  • COOT (Manual) (Type: ccp4_setup before using coot)
  • O (Manual) : ono
  • PYMOL (Manual) : pymol
  • RASMOL (Manual) : rasmol
  • VMD (Manual) : vmd
  • MOLMOL (Manual) : molmol

Structure Analysis

  • XtalView (Manual) : xtalmgr : xfit
  • COOT (Manual) (Type: ccp4_setup before using coot)
  • O (Manual) : ono
  • CCP4 (Manual) (Type: ccp4_setup before using)
  • PYMOL (Manual) : pymol
  • VMD (Manual) : vmd
Web-Based Analysis Services
  • PDB (GO)
  • MOLPROBITY (GO)
  • 3DNA (GO)
  • Curves-DNA (GO)
  • PROTSKIN
  • CONSURF (GO) Protein-protein interactions
  • PIPE (GO) Protein-protein & Protein-DNA interactions
  • SPPIDER (GO) Protein-protein interactions
  • PINUP (GO) Protein-protein interactions
  • PPIS (GO) Protein-protein interactions
  • CASTp (GO) Binding pockets
  • ProSurf (GO) Protein-protein interactions
  • PocketFinder (GO) Binding pockets
  • PDBsum
  • LIGPLOT
  • PKAPRO (GO)
  • CSU (GO)
  • NACCESS (GO) SASA
  • ACCESS (GO) SASA
  • GetArea (GO) SASA

DIP User Group Archive

Dear friends,

Mac Science's DIP systems have now been in several crystallography laboratories in the US and Europe for several years. We have formed an unofficial DIP user group with the approval of Mac Science and Nonius.  The goal and purpose of this group is to help each other with our research applications, and share any insights we may have in using the DIP systems.

Click here if you want your email address included in the list below. Tell us what system you have, and add any other information, links etc. that you would like to be included in the list below. Email addresses and other links are only included with the users permission.

An email list server for DIP users has been set-up. To automatically enroll send an email (or click on the line below) with the following enclosure:
add your_address@your_hostname dip-users

Sincerely yours

Mark  A. White
white@xray.utmb.edu
July, 1996

Mail to all DIP User Group members.
DIP2020k-12b  Yale U. Thomas Steitz , 
DIP2020k-12b  Salk Inst. S. Choe, Joe Noel, 
DIP2020k-12b  SUNYAB  Philip Coppens , Mike Carducci 
DIP2020k-12b    Alexander Wlodawer , 
DIP2030k-12b  BCM Florante A. Quiocho , Bill Meador , 
DIP2020k-12b  Fox Chase C.C. Jan Feng , Chiquito Crasto , 
DIP2020kNW-12b UTSWMED Johann Deisenhofer , Zbyszek Otwinowski , 
DIP2020kNW-12b  UVC Wladek Minor, 
DIP2030hVLM-16b  UTMB Robert O. Fox , Stanley J. Watowich, Edmund W. Czerwinski, Mark A. White 
DIP2030kVLM-16b  UAB Mark Walters , Randy Mann , 
DIP2030kVLM-NW-16b  TA&M Jim Sacchetini , Edgar Meyer , Stan Swanson , 
DIP2030-NW-16b  UTSWMED Steven Sprang , 
DIP2020-12b   UNC Chapel Hill Otto Zhou , 
DIP1030V-16b   NRL Carl Krandel , 
DIP2030-NW-16b  U. Alberta Michael James , 
DIP2030-NW-16b  Wasington State U. Wim Hol , 
DIP2030-NW-16b  St. Judes H. Steve White , Charles Ross , 
DIP-2030 & 
multi-wavelength XRG
 Salk Inst. S. Choe
DIP2030H-NW-16b  Umea University  Uwe H. Sauer , 
DIP3000 , DIP2000  Himeji Institute  Noritake Yasuoka , 
DIP2020K  LG Chem., Ltd  Sangsoo Kim , 
DIP2020K-16b  Rhone-Poulenc  Vincent Mikol , 
DIP2030H-16  Institut fuer Biochemie  Karsten Niefind , 


 

DIPUser News

07/96  Mac Science's newest high-speed DIP2030 released.
 
    The new system offers faster 155 sec. readout, 20 sec. erasure and quick 30 sec. interchange speeds.  Improvements in the hardware include a new ethernet interface with full 32MB buffering of the image.
1996 Short Magnetic Mount for Kappa
 
    Nonius developes new short Limbo magnetic mount goniometer head.  This head allows easy magnetic mounting to the 48 mm IUCr standard goniometer length of the DIP mini-kappa.
11/98 Mac Science WEB Site.
 
    Mac Science opens it's www.macscience.co.jp catalog site.  Now you can access the latest developments at Mac Science directly from a WEB site.
11/98  New Generator- Multi Wavelength.
 
    Mac Science's new multi-wavelength (MW-SRA) x-ray generator sees it's North American debut at the Salk Institute in San Diego CA.  The new Salk MW-SRA features Au,Cu, and Cr targets ,on the same anode, which are interchangable without breaking vacuum.
11/98 New Radial Calibration:
    J. Appl. Cryst. article by Mark A. White, Stanley J. Watowich, and Robert O. Fox of   UTMB  explains how the DIP user can easily create and apply a new radial calibration.  This technique offers a tool for recalibration of the DIP scanner, and a diagnostic for changes in detector sensitivity. This technique was developed prior to the new flood-field calibration applied to all new DIP scanners from 1996.  The author believes that this technigue offers the end-user a simpler more robust calibration and diagnostic tool than a flood field type calibration.
     
1/99 Nonius DIP2000 users group formed
    DIP2000 users notes, hints, and free software upgrades are available to Nonius's DIP2000 users group members.  To become a member simply go to the Nonius home page and click on users pages.

1/99    New Xpress software released: version 3.2.3

    The new version of MacScience's Xpress software offers additional utility and some bug fixes.  Members of the Nonius DIP users group can freely download the new software.

Other News:

NEWS The X-Ray Crystallography Newsgroup ,
NEWS Biomolecular Crystallography Newsgroup ,

HOW TO: Tips on Using the DIP

HOW to use the Pseudo-2-θ IP Offsetangle (PTO)

The  rotation of the IP with this ofset can be included in either the film rotation or cassette rotz parameters. We prefer the latter. The following are the equations we use to calculate the correct DENZO parameters.

Xbeam= Xbeam(0) - R ( 1 - Cos( PTO ) )          R = 140 mm DIP2020
Ybeam = Ybeam(0) - R  Sin ( PTO )          R = 200 mm DIP2030
Cassette rotz = rotz(0) - PTO           PTO is in degrees

Note that the sign of PTO may vary with DIP version ( Weissenberg vs. NW models, left vs. right hand).  If your R-merge shows a significant increase when using PTO see the New Radial Calibration. - M. A. White


Contact Mac Science

Mac Science and Enraf-Nonius are now owned by Bruker. The Nonius site has remained available for several years, the Mac Science site has been replaced by the link below. Bruker no longer offers detectors based on IP technology, but is actively maintaining the systems sold previously by Nonius and Mac Science.

Nonius Logo

Enraf Nonius (Now Bruker-AXS)

Mac Science Co. Ltd. logo

Mac Science Co Ltd: Japan (Now Bruker-AXS-Japan)