SHARP User Manual | previous next |
Appendix 2 |
Copyright | © 2001-2006 by Global Phasing Limited |
All rights reserved. | |
This software is proprietary to and embodies the confidential technology of Global Phasing Limited (GPhL). Possession, use, duplication or dissemination of the software is authorised only pursuant to a valid written licence from GPhL. | |
Documentation | (2001-2006) Clemens Vonrhein |
Contact | sharp-develop@GlobalPhasing.com |
Note : we highly recommend running the various programs through the interface - at least to get started and to make sure the whole installation is correct. Furthermore, if you run the programs outside the interface, various links will be setup differently, and you might not be able to view some results through the external viewers provided with Sushi.
You also need to know the architecture you're running on. Currently, the following architectures are available:
Name | Description |
---|---|
linux | Intel/Linux |
We will assume, that you want to keep all files and results within the sharpfiles directory structure. This way it is still possible to view and maintain results through the interface. However, you can also run the various programs in any directory. As an example, lets assume your project is called "Lysozyme-MAD-X31" and you're starting with the first run.
The following examples are all given as Bourne shell (sh): they should also be correct for shells like bash or ksh. You can easily change them to csh or tcsh syntax.
You need to get a few files/links into place. This is done by creating a directory Lysozyme-MAD-X31.1 (e.g. in ~/sharpfile/logfiles). Inside this new directory, create the following files/links:
Please note that from SHARP 2.0.0 onwards, the OBSFILE keyword is located in the general (top) section of the SIN file. However, for backwards compatibility to previous SHARP versions, the older syntax (with it being defined at the BATCH level) is still supported.
Alternatively, create a file with name REFL01.mtz : this is the MTZ reflection file SHARP is using. It should contain all the columns referenced in the SIN file. If this file is present in the current directory, SHARP will use this instead of the values given in the SIN file via the DATAFILES/OBSFILE keywords..
Use the following small script as an example and run it within the newly created Lysozyme-MAD-X31.1directory:
#!/bin/sh # set BDG_home: BDG_home=/where/ever/sharp # define SHARP binary: EXE=$BDG_home/bin/linux_exe/sharp export BDG_home $EXE > LIST.html 2> STDERR |
You need to prepare a directory and an input file. This is done by creating a directory Lysozyme-MAD-X31.1 (e.g. in ~/sharpfile/logfiles). Inside this new directory, create the following file:
Use the following small script as an example and run it within the newly created Lysozyme-MAD-X31.1directory:
#!/bin/sh # set BDG_home: BDG_home=/where/ever/sharp # command (this should be there): CMD=$BDG_home/bin/sharp/detect.sh export BDG_home $CMD > LISTautoSHARP.html 2>&1 |
You need to prepare a directory and an input file. This is done by creating a sub-directory solo_50.0pc within your Lysozyme-MAD-X31.1 directory (which is in ~/sharpfile/logfiles). Additionally, create the following file:
Use the following small script as an example and run it within the Lysozyme-MAD-X31.1 directory:
#!/bin/sh BDG_home=/where/ever/sharp CMD=$BDG_home/bin/sharp/solomon.sh export BDG_home $CMD > solo_50.0pc.log.html 2>&1 |
You need to prepare a directory and an input file. This is done by creating a sub-directory wARP_50.0pc within your Lysozyme-MAD-X31.1 directory (which is in ~/sharpfile/logfiles). Inside this new directory, create the following files:
Use the following small script as an example and run it within the Lysozyme-MAD-X31.1/wARP_50.0pc directory:
#!/bin/sh BDG_X="sharp" BDG_home=/where/ever/sharp CMD=$BDG_home/bin/sharp/arpwarp.sh export BDG_home . $BDG_home/.bdgrc $CMD > ../wARP_50.0pc.log.html 2>&1 |