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Partha<br>
<br>
Modified residues can be handled by eLBOW. Run<br>
<br>
phenix.elbow file.pdb --do-all --opt<br>
<br>
to get a CIF file to pass to phenix.elbow. The option --opt is
optional but recommended.<br>
<br>
Nigel<br>
<br>
On 10/1/2007 5:59 AM, Partha Chakrabarti wrote:
<blockquote
cite="mid:1cec38800710010559n64d0164sa808a5b05d2f8d4d@mail.gmail.com"
type="cite">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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
href="mailto:pchakra@nimr.mrc.ac.uk">pchakra@nimr.mrc.ac.uk</a><br>
> Phone: + 44 208 816 2515<br>
> _______________________________________________<br>
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</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 moz-do-not-send="true" href="mailto:pchakra@nimr.mrc.ac.uk">pchakra@nimr.mrc.ac.uk</a><br>
Phone: + 44 208 816 2515
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax : 510-486-5909
Email : <a class="moz-txt-link-abbreviated" href="mailto:NWMoriarty@LBL.gov">NWMoriarty@LBL.gov</a>
Web : CCI.LBL.gov</pre>
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