SCSB
X-ray
Software
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
Crystallization
Data Processing
- HKL (Manual) : hkl2000 : denzo : dip : xdisp :scalepack
- CCP4 (Manual) (Type: ccp4_setup before using)
- PROTEUM (Manual) (Windows Only for Bruker CCD)
- XPRESS (Manual) (SGI Only for DIP2030)
Structure Solution
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
- MIFit (Manual) : New XtalView uses some CCP4
- COOT (Manual) (Type: ccp4_setup before using coot)
- CCP4 (Manual) (Type: ccp4_setup before using)
- CCP4MG (Manual)
- O (Manual) : ono
- RAPPER (Home
Molecular Graphics
- XtalView (Manual) : xtalmgr : xfit
- MIFit (Manual) : New XtalView uses some CCP4
- COOT (Manual) (Type: ccp4_setup before using coot)
- Chimera (Manual) : chimera
- O (Manual) : ono
- PYMOL (Manual) : pymol
- RASMOL (Manual) : rasmol
- VMD (Manual) : vmd
- MOLMOL (Manual) : molmol
Structure Analysis
- XtalView (Manual) : xtalmgr : xfit
- MIFit (Manual) : New XtalView uses some CCP4
- COOT (Manual) (Type: ccp4_setup before using coot)
- O (Manual) : ono
- CCP4 (Manual) (Type: ccp4_setup before using)
- PYMOL (Manual) : pymol
- VMD (Manual) : vmd
- PDB (GO)
- MOLPROBITY (GO)
- 3DNA (GO)
- Curves-DNA (GO)
- PROTSKIN
- CONSURF (GO) Protein-protein interactions
- PIPE (GO) Protein-protein & Protein-DNA interactions
- HADDOCK (GO) Protein-protein interactions
- PINUP (GO) Protein-protein interactions
- PPIS (GO) Protein-protein interactions
- SPPIDER (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
SAXS
Small Angle X-ray Scattering
Software for Small Angle X-ray Scattering
- PRIMUS (Manual) :Data Processing & GUI (WINDOWS)
- PRIMUS will work on LINUX using WINE
- wineconsole /home/*****/.wine/drive_c/ATSAS/primus.exe
- BUNCH (Manual) :pre_bunch.l86:bunch8.l86: Rigid body Fitting
- GNOM (Manual) :gnom45.l86: Rg Calculator
- GASBOR (Manual) :gasbor22i.l86:gasbor22p.l86: Molecular Envelope
- SASREF (Manual) :sasref6.l86: Modelling of multisubunit complexes
- DAMMIN (Manual) :dammin53.l86:: Random Atom Model
- CRYSOL (Manual) :crysol26.l86: Rigid body Fitting
- EOM (Manual) Ensemble of Models
- RANCH :ranch13.l86: Ensemble builder
- GAJOE :gajoe13.l86: Ensemble Optimization
- Glatter & Kratky (SAXS Textbook) :(eds. O. Glatter & O. Kratky, 1982
- MES (Manual) :mes DataFileList: Ensemble Optimization
- Andrej Sali's Tools (UCSF)
- BioXTAS project
- RAW (Sourceforge)
- USAXS Jan Ilavksy
SAXS WEB
DIP User Group Archive
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
mawhite@utmb.edu
July, 1996
|
|||
|---|---|---|---|
| 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 , | |
|
|
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
- 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.
- 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.
- 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.
- 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.
- 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.
- 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
