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Generate XDS.INP (view source)

Revision as of 09:42, 16 July 2011

377 bytes added ,  09:42, 16 July 2011
reorganize webpage
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This script generates XDS.INP based on a list of frame names supplied on the commandline.
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This script generates XDS.INP based on a list of frame names supplied on the commandline. It currently works for MarCCD, ADSC and Pilatus 6M detectors; since this is just a bash script, extension to other detectors is very easy.
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Currently works for MarCCD, ADSC and Pilatus 6M detectors. Also supports bzip2-ed frames (when specifying the frame names, leave out the .bz2 extension, as [http://strucbio.biologie.uni-konstanz.de/~dikay/XDS_html_doc/html_doc/xds_parameters.html#NAME_TEMPLATE_OF_DATA_FRAMES= documented] for XDS!).
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== Usage ==
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Installation: ask your system adminstrator to cut-and-paste it into e.g. /usr/local/bin/generate_XDS.INP , and to make it "executable". Usage is then just (don't forget the quotation marks!):
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Usage is just (don't forget the quotation marks!):
 
  generate_XDS.INP "frms/mydata_1_???.img"
 
  generate_XDS.INP "frms/mydata_1_???.img"
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But you may also just cut-and-paste the script from this webpage into e.g. your home directory; the filename should be generate_XDS.INP. After creating the file, make it executable - e.g. if it's in your $HOME, use:
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XDS [http://strucbio.biologie.uni-konstanz.de/~dikay/XDS_html_doc/html_doc/xds_parameters.html#NAME_TEMPLATE_OF_DATA_FRAMES= supports] bzip2-ed frames. Thus, when specifying the frame name parameter of the script, you should leave out any .bz2 extension.
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chmod +x ~/generate_XDS.INP
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After that, you can just run it in the same way:
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~/generate_XDS.INP "frms/mydata_1_???.img"
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By using your own file, you can easily update to the latest revision, or even change the script, without having to bother the system administrator.
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Instead of cut-and-paste, you could try
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== The script ==
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wget http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP -O - | awk '/^#/,/rm -f tmp1 tmp2/' | \
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  sed -e s/\&nbsp\;/\ /g -e s/\&gt\;/\>/g -e s/\&lt\;/\</g -e s/amp\;//g -e s/\&quot\;/\"/g > generate_XDS.INP
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to copy the script from this website into the file generate_XDS.INP in your current directory.
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This is the script:
   
<pre>
 
<pre>
 
#!/bin/bash
 
#!/bin/bash
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rm -f tmp1 tmp2  
 
rm -f tmp1 tmp2  
 
</pre>
 
</pre>
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== System-wide or personal installation ==
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Ask your system adminstrator to cut-and-paste the script into e.g. /usr/local/bin/generate_XDS.INP, and to make it "executable".
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But you may also cut-and-paste the script from this webpage into a file in e.g. your home directory; the filename should be generate_XDS.INP. After creating the file, make it executable - e.g. if it's in your $HOME, use:
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chmod +x ~/generate_XDS.INP
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After that, you can just run it in the same way  as if it were installed in your $PATH:
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~/generate_XDS.INP "frms/mydata_1_???.img"
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By using your own file, you can easily update to the latest revision, or even change the script, without having to bother the system administrator.
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== Generating generate_XDS.INP from this webpage ==
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Instead of cutting-and-pasting the lines of the script, you (or the system administrator) could just cut-and-paste the following four lines
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wget http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/generate_XDS.INP -O - | \
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  sed -e s/\&nbsp\;/\ /g -e s/\&gt\;/\>/g -e s/\&lt\;/\</g -e s/amp\;//g -e s/\&quot\;/\"/g | \
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  awk '/^#/,/rm -f tmp1 tmp2/' > generate_XDS.INP
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chmod +x generate_XDS.INP
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to copy the script from this website into an executable file generate_XDS.INP in your current directory.
Kay
Bureaucrats
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