Hi Peter,<br><br>Thanks a lot for your suggestions. Its close but not completely happy yet.<br>So, I generated the file as you suggested, several of the commands are understandable, and I can run it after modification as:<br>
<br>$ phenix.refine <parameter.def<br><br>but would be easier if there is a scrip for phenix.refine as available for SOLVE/RESOLVE. Could you point me to the not so easy way of doing that? <br><br>One particular problem seems to be modified residues, in my case, a phosphothr (TPO), had to delete the phosphate and rename TPO as THR.. is there any wayout?
<br><br>Best, Partha<br><br><br><br><div><span class="gmail_quote">On 9/28/07, <b class="gmail_sendername">Peter Zwart</b> <<a href="mailto:PHZwart@lbl.gov">PHZwart@lbl.gov</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
The easiest way is to have a parameter file that you edit.<br>The easiest way to get a parameter file is by typing<br><br>phenix.refine <model> <data> --dry_run<br><br>and use the subsequently generated ???_refine_001.eff file.
<br><br>rename that eff file to something like<br><br>parameters.def<br><br>which you can use for subsequent customisations and editing of parameters.<br><br>Not ethat every time you finish a refinement job, a new def file is
<br>generated of rthe next round, updating the model info for further<br>rounds of refinement.<br><br><br>P<br><br><br><br><br><br><br><br><br><br><br><br><br><br>2007/9/28, Partha Chakrabarti <<a href="mailto:ppchak@gmail.com">
ppchak@gmail.com</a>>:<br>> Hi,<br>><br>> I am wondering if one can have master scripts (C shell) for the macro cycle<br>> of phenix.refine that can be used from the command line. It is easier to<br>> comment out an option than having to type the whole thing.. has anybody
<br>> tried it? Similar scripts exist for solve/resolve and phaser..<br>><br>> I should not say it, I am myself not adverse to using the GUI, it is just<br>> easier when the poor postdoc sits with the boss.. typically I face the
<br>> question: where is the script file & where is the log file :))<br>><br>> Cheers, Partha<br>><br>><br>> --<br>> MRC National Institute for Medical Research<br>> Division of Molecular Structure
<br>> The Ridgeway, NW7 1AA, UK<br>> Email: <a href="mailto:pchakra@nimr.mrc.ac.uk">pchakra@nimr.mrc.ac.uk</a><br>> Phone: + 44 208 816 2515<br>> _______________________________________________<br>> phenixbb mailing list
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http://www.phenix-online.org/mailman/listinfo/phenixbb</a><br></blockquote></div><br><br clear="all"><br>-- <br>MRC National Institute for Medical Research<br>Division of Molecular Structure<br>The Ridgeway, NW7 1AA, UK<br>
Email: <a href="mailto:pchakra@nimr.mrc.ac.uk">pchakra@nimr.mrc.ac.uk</a><br>Phone: + 44 208 816 2515