7. Available crystallographic software
All five
user’s computers have the same set
of crystallographic software to integrate and scale experimental data
and to solve and refine the structure. All software packages, as
provided by SBGrid, are located under /programs. Nearly all
crystallographic software packages are installed on our computers,
always try to find it.
Below are the descriptions of the most often used crystallographic packages:
HKL2000 – type "hk2000" from the directory where you have write permission and where you want to place your results. The hard copy manual is available on the beamline. Two comments : first, the main failure during the autoindexing is the wrong position of the direct beam – use web-based "NE-CAT Tools" to find the exact direct beam position at the specific distance – write it down and input into "Site Configuration" menu; second, make sure the distance and the energy read from the file headers are correct (in the MAIN tab of HKL2000 window), change them if necessary. Don’t forget to set proper blind region around the beamstop shadow. Don’t reuse HKL2000 window for your next project, close it and open the new one in a different directory.
If you want to run old-fashion xdisp/denzo/scalepack, type "x315" (alias) / "denzo" , or "scalepack" on a command line. The site definition file is "/usr/local/hklint/24ID_315a/def.site"
LABELIT – Very powerful software for the indexing (very challenging cases); collect two images separated by 90o and type "labelit.screen <directory_with_images> 1 90 " - specify a directory path followed by one or two image numbers.
CCP4/CCP4i – type "ccp4i" or any routine name you need to run on a command line - $CCP4/bin is automatically in your path. To get help use "man" for any major routine. The default installation is version 6.o-beta. To use old version you need to source the old setup file in corresponding directory.
SOLVE/RESOLVE – go to the new directory, prepare the script to run (either copy and edit one from $SOLVEDIR/examples_solve/p9 or use your own magic one). You may also type either "solve" or "resolve" from the command line. The manual/ help is available online only by typing "solvehelp" or "resolvehelp".
ARP/wAPR – may be run either as a part of CCP4i or from the command line. Online help is available from the author’s web site and a short hard copy manual is in the binder by user’s computers.
HKL2MAP – This is an easy GUI for running shelxc, shelxd and shelxc to determine heavy atom sub-structure and preliminary phase calculations. Command to run this program is "hkl2map" and a window will pop-up with useful hints to run it, during the run it’s also very handy to check the graphics result.
CNS v.1.3 – Type "cns< your_input-file.inp>output.log" . Online help, input files, tutorials, etc are available by typing "cns_web". To convert HKL2000 .sca reflections file to CNS format type "to_cns". (if not in the path, use "locate" to find it )
PHENIX v.1.4 – Type "phenix" on the command line to start GUI for structure solution and refinement. The help is available in a separate window. There are several automated Wizards tab on the PHENIX GUI. -AutoSol -- Structure solution by MAD/SAD/MIR (Inputs: X-ray intensities; sequence file, scattering factors; Output: experimental phases, preliminary density modification and model)-AutoMR -- Molecular replacement (Inputs: MTZ file with FP, SIGFP; one or more ensembles of aligned structures to place in cell; Output: Ensembles placed in cell.)-AutoBuild -- Iterative model-building and refinement (Inputs: MTZ file with FP, SIGFP, optional phases/HL coeffs or model; Output: Partially-refined model and density-modified phases) -LigandFit -- Ligand fitting (Inputs: PDB file with ligand in any stereochemically allowed conformation; MTZ file with FP; PDB file with partial structure without ligand; number of copies of ligand to find; Output: Copies of ligand fitted to difference density). The wizard will guide you and ask for necessary inputs. The wizard is green when running, blue when stopped, and red if an error has occurred.
O and COOT – your choice for graphics (pymol is available thru PHENIX). To start type either "o" or "coot". Both programs support stereo on CRT monitor only on nec2 (the most left user’s computer) and zeus (stereo glasses are behind the monitor). To have stereo for O you should type "setenv STEREO on" first.
SHARP – Open a web browser. Connect to http://machinename:8080, where machine name is the name of the computer you are working on. SHARP is installed on nec1, nec3, bromine, mercury, sulfur, uranium, iron, copper and zeus. For example, on nec1 you browse to http://nec1:8080. This opens a login window. Login with "necat" and the password given to you by the beamline scientists. This will open the sharp user interface.
The software may complain that HTTP server is not running: -- please execute from the command line : ~necat/sharp/adm/bin/restart_server. Now you should be able to connect to http://machinename:8080. (username – necat, the password is the same as login necat password)
SnB - Shake-and-Bake, a dual-space direct-methods procedure for determining crystal structures from X-ray diffraction data. SnB v2.2, provides a graphical user interface for (i) computing normalized structure-factor magnitudes, (ii) the main Shake-and-Bake phasing algorithm, and (iii) visualization and molecule-editing facilities. Type "SnB"; examples are in /programs/l/snb/2.2pl1/examples/
BnP -- BnP is a protein structure determination package with a graphical user interface. The interface controls and runs processes required for the complete solution of protein crystal structures in a point-and-click manner. BnP's main function is to couple the direct-methods program BnP, used to determine heavy atom/anomalous scatterer substructures, with the protein-phasing package PHASES, used to determine and refine protein phases. Type "BnP" ; examples are in /programs/l /bnp/1.02/examples
SGXPRO - very powerful automated software package with easy to use GUI. The GUI automatically manages communication between different software packages and permit to build many different structure determination strategies with different choice of parameters (intelligent default parameters are always present in all steps). Everything is done in a user-friendly environment with automatic generation of program-specific input files and file formats conversions. Since the software is optimized for parallel processing, it is possible to generate many input file and several different pathways to sample the range of various input parameters (like different resolution cut-offs, number of sites, error levels etc) and finally submit a big job to a powerful computer cluster. SGXPRO is based on the plug-in design and currently support the following software: SHELXD, ISAS, SOLVE/RESOLVE, MAID, AMORE, BEAST, EPMR, DM, SOLOMON, XTALVIEW and ARP/wARP through CCP4i interface. Plug-ins for CNS, Refmac5, SnB and scaling are currently under development. NE-CAT has a license for SGXPRO to be used on our local computers.
Every effort is made to install the newest version of the software as soon as possible, though some delay may exist. The necat .cshrc file is not writable by necat users; if you need to change any environmental variables you can do it manually for your local session only – contact beamline personnel with your suggestions/comments.
Under active development is the web-based automated daemon (called RAPD) for initial data processing, calculation of optimal strategy for data collection and integration/scaling of data. All current features, access privileges and detailed instruction will be given by your support personnel.