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File Transfer
The prefered way to transfer files is through the secured file transfer protocal SFTP. sFTP Instructions
Data collected on the Raxis 4 can now be transfered to the UNIX cluster via ftp.
FTP Instructions
Backups and Downloads
Currently backups and/or downloads can be done with either 4mm DDS4 tapes, CD's or DVD's. The DDS4 and CD writer are located on REDWALL1 and the DVD burner is on Angelina. DVD's and CD's can be burned using the program K3B under Linux.
DVD/CD writing instructions on angelina.br.caltech.edu.
Data can also be transfered to the cluster via sftp. It is recommanded that you put your raw image files on one of the /temp disks on the linux boxes or the temp directories on the alpha's preferably the one you are working on. Please remember that files are deleted from the /temp directories every 3 days from the date they are written.
Data can now be stored for a longer period of time in /net/lindy1/imagestorage or on windows //lindy1/imagestorage. Please be aware that you should transfer the images to the /temp directory on the computer that you are processing your data on.
YOUR HOME DIRECTORY IS NOT TO BE USED FOR IMAGE STORAGE!
Available software
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DATA PROCESSING |
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| PROGRAMS |
DESCRIPTION |
COMMAND |
HKL Home page v1.98.2 (Xdisplay/Denzo/Sclaepack)
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Image data processing suite |
%xdisp "dectector format" filename (to view diffraction images.
%denzo (Program to process images)
%scalepack < "scalepack command file" > scale.logfile (Program to scale images.) |
| Mosflm 6.2.3 (Harry Powell's Help Page) |
Image data processing suite. Also distributed with CCP4 package |
%mosflm |
| Phenix |
Automated structure determination suite, from intesity data to final model |
%phenix |
| Elves |
Automated processing and phasing interface |
%elves "tell it what to do" |
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Phasing and structure determination |
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| CCP4 5.0.2 |
Suite of macromolecular crystallography programs from data processing to structure validation |
%ccp4i (To call up graphical interface |
| CNS v1.1 |
Program suite for inital phasing, refinement and basic structure validation |
%cns_solve < cns input file > cns.logfile |
| XtalView |
Package for structure solution by isomorphous replacement and model building |
%xtalmgr |
| 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 flile > 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 |
| Shake n Bake 2.2 |
Dirct methods procedure for crystal structure determination. Also good for finding substructures |
%SnB (on lindy's) |
| SHARP |
Heavy atom refinement and phase calculations |
From either windows explorer, netscape, or firefox
http://lindy2.br.caltech.edu:8080 |
| BUSTER |
Stucture determination from partial structures by Baysian statistical methods |
See Sharp
http://lindy2.br.caltech.edu:9292 |
| Phaser 1.3.1 |
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 |
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Utilities and Fitting |
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| ARP/wARP 6.1.1 |
Auto building program run through the CCP4 interface |
%ccp4i |
| Uppsala Software Factory (USF) |
A serise of utility programs for handling coordiate files, maps files etc... |
Type name of program at prompt.
example:
%mapman |
| Alwyn Jones O Related Pages |
Model and map visualization and building |
For 0 ver 9.x
%o900
O ver 10
%o10 |
| Coot |
Model and map visualization and building. Can do some on the fly optimization |
%coot |
| PyMOL |
Molecular model visualization |
%pymol |
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Analysis, Etc... |
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| GRASP |
Electrostatic surface calcualtion and visulazation |
Only available of SGI's.
%grasp |
| Molscript v2.0 |
Structure visualation |
%molscript2 |
| Raster 3D |
Program for generating high quality raster images of proteins or other molecules |
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| BobScript |
Robert Esnouf's extensions to MolScript version 1.4 |
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| 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 |
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Web Based Tools |
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| CASTp |
volume/cavity calculations |
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| UCLA Services |
Twinning test server,Verify 3D, etc... |
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| Molray |
Web interface to POV-Ray that produces graphics images from O plot files |
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Sample Denzo/Scalepack command files. These can be used as template command files for data processing with Denzo and Scalepack
Indexing and processing of frames - auto.dat and refine.dat
Scaling and merging of frames - scale.com
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