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Hi Kate,<br>
<br>
one can endlessly talk about this matter and there is a number of good
papers out there. <br>
<br>
At some point I spent significant amount of time trying to address the
questions you mention below. I selected all structures from PDB for
which NCS is available and re-refined them with and without NCS. My
goal was to answer this question: given a model and data, can I tell
for sure if I need to use NCS or it's better to refine without using
NCS. In the end I couldn't derive any reliable formula to be able to
decide if I need to use NCS or not. All I re-discovered was the old and
well known fact: if have have NCS, then lower the resolution, more
likely you want to use NCS -:) Obviously, at ~1.5A resolution the use
of NCS was only damaging. And ~2.0A is kind of "gray area".<br>
<br>
So this is why I wrote in my previous email that it is much easier,
quicker and reliable to just try both ways and see which one works
better, rather than waste time on speculating -:)<br>
<br>
Cheers,<br>
Pavel.<br>
<br>
On 8/25/2008 11:33 AM, Kate Kavanagh wrote:
<blockquote cite="mid:48B2FADE.8090909@mail.utexas.edu" type="cite">
<pre wrap="">I was wondering if there a consensus of when it is mandatory to use ncs
in refinement. Is is dependent on:
1. resolution?
2. data-to-parameter ratio?
3. difference between Rcryst & Rfree?
4. something else...
Or does one just do as Pavel states and try both ways ?
Regards,
Kate
Pavel Afonine wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Francis,
</pre>
<blockquote type="cite">
<pre wrap="">Also if anyone has a paper/protocol for NCS refinement, I'd love to
check it out (to figure out which map to fit to).
</pre>
</blockquote>
<pre wrap="">Just something to keep in mind... I always prefer to run two refinements
in parallel with and without using NCS. It's resolution (and
data-to-parameters ratio) dependent. I've seen a number of cases where
using the NCS is very beneficial and similar number of cases where it's
better to not use NCS (mostly at resolutions ~2-2.5A).
I would also check manually the NCS groups that are found by
phenix.refine automatically. I have some cases where automatic detection
did not yield a good selection.
Pavel.
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