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<p class=MsoNormal>- If we really want to keep "--unused-ok", then we
should probably make it less obvious to use for newbies. If an expert knows it
exists (which will be mentioned in the docs), then great - use it at your own
risk. But for new users it is often the first thing they see when they
mis-format they parameter files.<br>
<br>
<span style='color:#1F497D'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>I like that idea. <o:p></o:p></span></p>
<p class=MsoNormal><br>
- One day running phenix.refine will be matter of running one command or
hitting one button with no need to edit any parameters. That will be the day
when the *true* automation of refinement won. <br>
<br>
<span style='color:#1F497D'><o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'>Lofty goal, will this be reality before I retire? (-:<o:p></o:p></span></p>
<p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D'><o:p> </o:p></span></p>
<p class=MsoNormal><br>
Pavel.<br>
<br>
<br>
On 5/12/09 5:36 AM, Schubert, Carsten [PRDUS] wrote: <o:p></o:p></p>
<pre>Couple of comments:<o:p></o:p></pre><pre><o:p> </o:p></pre><pre><o:p> </o:p></pre><pre> <o:p></o:p></pre>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><pre>I keep seeing people having trouble refining their structures in<o:p></o:p></pre><pre> <o:p></o:p></pre></blockquote>
<pre>phenix.refine just because they were using "-->unused-ok" option. <o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Well, with every powerful tool come caveats. The unused_ok option is a<o:p></o:p></pre><pre>expert option and if people who have difficulties understanding what<o:p></o:p></pre><pre>they are doing use it and encounter problems then it begs the question<o:p></o:p></pre><pre>why expert users need to suffer the consequences of their inabilities. I<o:p></o:p></pre><pre>use this option often and it is warranted in the current environment in<o:p></o:p></pre><pre>which phenix goes through a lot of revisions, which break compatibility<o:p></o:p></pre><pre>with previous versions, but provide new/better functionality I'd like to<o:p></o:p></pre><pre>use. And yes, if you are doing a couple of structures a day, reediting<o:p></o:p></pre><pre>the parameter file(s) is a serious drag.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre> <o:p></o:p></pre>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><pre>Finally, I don't understand what the trouble is to run this command:<o:p></o:p></pre><pre>phenix.refine --diff-params your_old_parameters.def ><o:p></o:p></pre><pre> <o:p></o:p></pre></blockquote>
<pre>your_new_parameters.def<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>It is NOT usable in a automation environment. Since phenix goes through<o:p></o:p></pre><pre>so many releases, which change the parameter file and bails by default<o:p></o:p></pre><pre>if the parameter file does not match the current version, automation is<o:p></o:p></pre><pre>difficult to achieve. Correct me if I am wrong, but I believe it would<o:p></o:p></pre><pre>almost be impossible to pick up a previous refinement done with a old<o:p></o:p></pre><pre>phenix version again via an automated approach if the parameter file has<o:p></o:p></pre><pre>changed and phenix bails. Granted I could freeze the phenix version used<o:p></o:p></pre><pre>for automation and could maintain a couple of different versions for<o:p></o:p></pre><pre>different purposes, but that quickly becomes impractical. <o:p></o:p></pre><pre><o:p> </o:p></pre><pre>So in essence, for the "high-throughput-bleeding-edge-junky-users" the<o:p></o:p></pre><pre>--unsed_ok option is essential and I hope that it remains.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Cheers.<o:p></o:p></pre><pre><o:p> </o:p></pre><pre> Carsten<o:p></o:p></pre><pre> <o:p></o:p></pre><pre><o:p> </o:p></pre><pre>_______________________________________________<o:p></o:p></pre><pre>phenixbb mailing list<o:p></o:p></pre><pre><a
href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><o:p></o:p></pre><pre><a
href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a><o:p></o:p></pre><pre> <o:p></o:p></pre></div>
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