Computer and Software Information

File Transfer

The preferred way to transfer files is through the secured file transfer protocol SFTP.
sFTP Instructions

Backups and Downloads
Users are responsible for there own downloads of image data and backups of image data. The images on the data collection computer will be deleted when storage space is need. The oldest images will deleted first.

Available Software
  Data Processing  
Programs Description Command
D*Trek Rigaku's Information Page Image data processing suite. Can be run through Crystal Clear or separately.
Mosflm_7.0.1 (Harry Powell's Help Page) Image data processing suite. Also distributed with CCP4 package. %mosflm
Phenix Automated structure determination suite, from intensity data to final model. %phenix

  Phasing and Structure Determination  
CCP4_6.1.1 Suite of macromolecular crystallography programs from data processing to structure validation. %ccp4i (To call up graphical interface
CNS_v1.2 Program suite for initial phasing, refinement and basic structure validation. %cns_solve < cns input file > cns.logfile
Main Visualization from initial phasing, model building, refinement and validation interface. %mainps
SOLVE 2.0.9/RESOLVE Automated crystallographic structure solution for MIR, SAD, and MAD/Density modification, automated model building etc.... %solve < solve command file > solve.logfile
%resolve < resolve command file > resolve.logfile
SHELX Dirct methods procedure for crystal structure determination. Also good for finding substructures. High resolution least squares refinement. %shelxs filename  (structure solution
%shelxl filename (structure refinement)
%shelxpro filename (macromolecular input interface)
See hkl2map for ShelxC, D and E interface.
HKL2MAP Interface to ShelxC, D and E %hkl2map
SHARP Heavy atom refinement and phase calculations. From either windows explorer, netscape, or firefox 
BUSTER Structure determination from partial structures by Bayesian statistical methods. See Sharp
Phaser 2.1.2 Automated molecular replacement program. Run through CCP4 or Phenix suites. %phaser <command file>
EPMR Molecular replacement program using an evolutionary search algorthim. %epmr filename.cel filename.hkl filename.pdb

  Utilities and Fitting  
ARP/wARP 7.0.1 Auto building program run through the CCP4 interface. %ccp4i
Uppsala_Software_Factory(USF) A series of utility programs for handling coordinate files, maps files etc... Type name of program at   prompt.
example:
%mapman
Alwyn Jones O Related Pages Model and map visualization and building. Current version is 12.0
Coot Model and map visualization and building. Can do some on the fly optimization. %coot
PyMOL Molecular model visualization. %pymol

  Analysis, Etc....  
Raster3D Program for generating high quality raster images of proteins or other molecules.  
Promotif v.3 Analysis of structural motifs. %promotif filename.pdb
Whatcheck Protein verification tools. %whatcheck filename.pdb
Procheck Protein verification tools. Usually run through the CCP4 interface. %procheck resolution filename.pdb

  Web Based Tools  
CASTp           volume/cavity calculations.  
UCLA Services Twinning test server,Verify 3D, etc..  
Molray Web interface to POV-Ray that produces graphics images from O plot files.  

Last updated 3/24/2009 by LMT