[phenixbb] hydrogens in riding model create steric clashes after refinement

[amadrona at uci.edu]

>   Hi Yarrow,
>
>> I was given two sets of coordinates (my model and a pdb for Iron atoms)
>> I
>> included this new model in the next round of refinement but I did not
>> include the pdb for the Iron atoms.
>
> this is strange... Why you decided to use a worse model (an incomplete
> model without Iron atoms) in refinement?
>
>> I ran refinement with the folowing parmeter file:
>>
>> refinement.main.ordered_solvent = true
>> #refinement.main.ordered_solvent.mode=filter_only
>> refinement.refine.strategy = individual_sites+individual_adp
>> #refinement.refine.adp.individual.isotropic = "chain W"
>> refinement.output.prefix = CIN4_refine
>> refinement.output.serial = 18
>> refinement.output.write_def_file = True
>
> I presume you refine non-H and non-water atoms as isotropic and the rest
> as anisotropic.
>


Acutually I refined everything anisotropic.  Previously I refined waters
isotropically but my Rwork and Rfree increased.  Is this a bad idea?
BTW Thanks for the tip on iding clashes with the phenix GUI.)




>> resolution is 1.37A with close to 400,000 unique observations (obs/param
>> is still about 4)
>> Stats:
>>            Rwork    Rfree   bonds   angles
>> start:    .1444     .1723  .016     1.617
>> end:      .1371     .1657  .010     1.301
>
> The numbers look good given the resolution.
>
>> I also ran wxu and wxc optimization from the command line.
>
> Good idea.
>
>> I know that the defualt is "riding-model" so that the hydrogen atoms are
>> not refined.  However, I thought that the program would be able to avoid
>> steric clashes.
>
> Using hydrogen atoms in refinement helps to reduce the amount of clashes
> but does not guarantee to eliminate them completely. I would just check
> all them one by one - which is very easy using PHENIX GUI: in fact,
> PHENIX GUI will give you the list of clashes (run Comprehensive
> Validation tool) and then you just click on each of them and this will
> automatically bring it zoomed in Coot. So, it should be a quick and easy
> exercise. Then, once you are done with fixing them, just re-run the
> refinement.
>
>> There are also a handfull of hydrogens that
>> exist out in space that I decided to delete.
>
> This is weird and should not happen. I would find out how you got them.
>
> Pavel.
>
>
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