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Hi Lisa<br>
<br>
<blockquote type="cite"
cite="mid:0EAB2806-B8ED-4FDF-A266-4EC0DEFE7666@rug.nl">
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For the validation of my model to my map in phenix 1.17.1 I tried
to refine my shaken model (0.5Å) against my half map in phenix
real space refine. </blockquote>
<br>
first off, I think this way of validation is quite faulty
conceptually... How you know 0.5A is the best number and say not 0.7
or 0.3? By shaking the model, you validate the shaken (perturbed)
model, which is not the model you are publishing and reporting
statistics for. If you shake the model twice with same shake doze,
you will get two different models with the same amount of
perturbation, which means numbers you derive from such models can
(and likely will) be different. So... with this in mind I'm not
really seeing any use of such a validation approach; this does not
make sense to me at all!<br>
<br>
Instead, why wouldn't you just follow the standard validation
procedure, where you validate the model, the data and the
model-to-data fit? The Phenix tool for this is "Comprehensive
validation (cryo-EM)", it is available in the GUI and it is one stop
to do all of this. And if you want to find uncertainties in atomic
positions due to refinement converging to local minima, you can use
phenix.mia tool that will generate and refine many perturbed models
using exact same way and give you an ensemble of models that can
show local variations.<br>
<br>
All of the above described here:<br>
<br>
<a href="https://www.ncbi.nlm.nih.gov/pubmed/30198894">https://www.ncbi.nlm.nih.gov/pubmed/30198894</a><br>
<br>
Good luck and let me know if you have any questions!<br>
<br>
Pavel<br>
<br>
<blockquote type="cite"
cite="mid:0EAB2806-B8ED-4FDF-A266-4EC0DEFE7666@rug.nl">However,
whatever I try I get a weird behaviour in the FSC(Model-map), see
the image below. It seems not to be able to reach 0 in the
correlation, but keeps getting stuck at 0.1.
<div class=""><br class="">
</div>
<div class="">I tried various things to solve this, but
unfortunately nothing helps:</div>
<div class="">- Using the other half map</div>
<div class="">- Cut of the heterogeneous part of my model and map
and refine this</div>
<div class="">- Used refined data without using a mask for the
last iterations</div>
<div class="">- Used different resolutions to refine against</div>
<div class="">- Tried data from someone else in the lab (same
microscope, same imaging conditions), to check if I am doing
something wrong (this gave good results)</div>
<div class=""><br class="">
</div>
<div class="">When doing the same refinement in Refmac5 in ccpem
1.4 it does seem to work, however I would not like to switch
programs, because this will mess up my final model.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Lisa</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><img apple-inline="yes"
id="7B4F125F-A7F1-4729-B003-8F068DCFA996"
src="cid:part2.AF7A6054.EA00946A@lbl.gov" class=""></div>
<br>
</blockquote>
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