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Hi Jianghai,<br>
<br>
the answers to both of your questions are YES:<br>
<br>
- running phenix.refine with "wxc_scale=0" is essentially the same as
performing a pure geometry regularization (no Xray contribution is
accounted for). It is just less time efficient since even if you say
"wxc_scale=0", phenix.refine still compute all X-ray related things
like X-ray targets, R-factors, do bulk-solvent correction etc...<br>
<br>
- yes, phenix.refine will use all your custom bond definitions
regardless the value of "wxc_scale" parameter.<br>
<br>
Pavel.<br>
<br>
<br>
On 2/11/2008 12:43 PM, Jianghai Zhu wrote:
<blockquote
cite="mid:773838FE-017A-48C8-B57C-ABF4B94CD9B5@cbr.med.harvard.edu"
type="cite">
<blockquote type="cite">
<pre wrap="">2) Minimise the geometry of the protonated model from 1) withOUT X-
ray term with:
phenix.geometry_minimization --max-iterations=N input_h.pdb
</pre>
</blockquote>
<pre wrap=""><!---->
I have a question about geometry_minimization. I think wxc_scale = 0
is the same as phenix.geometry_minimization. But I have some external
bond definitions defined in the eff file. So if I use wxc_scale = 0
and phenix.refine, will those external bonds be imposed on the model
as the default geometries?
Thanks.
Jianghai
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</pre>
</blockquote>
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