<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html;charset=ISO-8859-1" http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi Carsten,<br>
<br>
the input refinement parameters and the input data (reflections and
model) are different things (in sense how they are treated, at least).<br>
<br>
All PDB files given at input, no matter how they are specified (in
command line or in parameter file) are accumulated into one file and
then this combined model is used in refinement. It is up to the user to
not specify one file multiple times and phenix.refine enforces this by
analyzing the clashes. <br>
<br>
As for parameters, if identical parameters are specified multiple
times, the last parameter is actually used.<br>
<br>
Ralf may have more comments on this.<br>
<br>
Pavel.<br>
<br>
<br>
Schubert, Carsten [PRDUS] wrote:
<blockquote
cite="mid889E20E3723D0C45A493DA5DA87D854ED5C26E@JNJUSRAGMS02.na.jnj.com"
type="cite">
<meta http-equiv="Content-Type" content="text/html; ">
<meta name="Generator" content="MS Exchange Server version 6.5.7653.2">
<title>Question about precedence of command line parameters vs. .def
file</title>
<!-- Converted from text/rtf format -->
<p><font face="Arial">Hi,</font>
</p>
<p><font face="Arial">I have a question / request about parameters
defined on the command line vs. defined in the .def file are handled.
Specifically the input.pdb.file_name parameter. I noticed that if I
have already a input.pdb.file_name defined in the .def file and call
phenix.refine with another pdb file, both files are loaded. If both pdb
files represent the same protein in different stages of refinement that
obviously causes the job to fail due to close non-bonding interactions.
</font></p>
<p><font face="Arial">I see how the loading of both pdb files can be
a desired feature, but I also recall reading somewhere that command
line params take precedence over .def files, which in turn takes
precedence over defaults. There seems to be some deviation from that
philosophy. </font></p>
<p><font face="Arial">For me this is more a work-flow issue (which
becomes important if one does to many structures per day ...) than a
bug. I'd really like to minimize the time spend on editing the def file
and just define new job parameters from the command line and have the
def file fill in the missing bits. This also would help future
automation we are implementing, because it would eliminate the need to
read and parse an existing .def. file. There are ways around this but
not as clean, but that is another matter ....</font></p>
<p><font face="Arial">Would it be possible to implement a switch
which would check for duplicate parameters on the command line vs. .def
file, give precedence to the command line and run the job like that?
That way we would not break the existing scheme, which other people may
have already grown accustomed too. Other suggestions are welcome too.</font></p>
<p><font face="Arial">Cheers,</font>
</p>
<br>
<p> <font face="Arial">Carsten</font>
</p>
<br>
<br>
<br>
<pre wrap="">
<hr size="4" width="90%">
_______________________________________________
phenixbb mailing list
<a class="moz-txt-link-abbreviated" href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>
<a class="moz-txt-link-freetext" href="http://www.phenix-online.org/mailman/listinfo/phenixbb">http://www.phenix-online.org/mailman/listinfo/phenixbb</a>
</pre>
</blockquote>
</body>
</html>