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. |