I assume that none of the things you tried have "worked" and you
probably got some kind of error message or otherwise results were
You must have the test set if you are using ML target in CNS. The
reason is that test set reflections are used to estimate sigmaA, and
without them the refinement target cannot be constructed.
Ed Berry is absolutely right that you need to use a different target.
Keep in mind that every structure in the PDB refined with CNS uses mlf
target. Other targets are implemented but never used.
Whether it's OK or not to run refinement at low resolution without
cross-validation may be debatable (e.g. if the model is first refined
with it, is it OK to turn cross-validation off as a last step when the
danger of overfitting is minimized), but what you want to do is unlikely
to gather majority support. I expect most people would agree that doing
refinement at low resolution without cross-validation is a dangerous
If you are willing to try, then Refmac and more recently phenix.refine
both allow refinement without cross-validation. Beware that if this is
something you plan to publish you are very likely to run into serious
opposition from reviewers.
On Tue, 2013-09-24 at 11:51 -0600, Crystal VanderZanden wrote:
> I'm trying to run minimize in cns, but I want to set it so it doesn't
> do an Rfree calculation, and so it will use all of my data in the
> minimization process. I have a small low-resolution dataset that
> doesn't have very many reflections, so I'm having to sequester about
> 20% of my data in order to run the Rfree calculation. Does anyone
> know how to turn the Rfree calculation off?
> Things I've tried:
> -making the minimize.inp target_bins=1 and flagging a very small
> percentage of my data as a test set
> -telling minimize.inp that my test_flag = 2 so no reflections would be
> marked as test
> -telling minimize.inp that my test_set=(none)
> Thanks in advance for any advice!
Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
------------------------------ / Lao Tse /