Regarding the riding hydrogens:
They are obviously not visible, but your protein in solution is also not visible but still has those weird riding hydrogens:-)
Use them, they are there. And ther was a recent compendium of neutron scattering in one of our favorite journals if you really want to see them.
Another rule to add:
You are 98% done with refinement of your structure, does it really matter - I mean from a functional/ biological perspective ?
Is it wrong to stop at some point ?
This of course implies you've already passed rule 3-5 from Robbie.
Just some Espresso-thoughts in the morning
Jürgen
......................
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab: +1-410-614-4894
Fax: +1-410-955-3655
http://web.mac.com/bosch_lab/
On Oct 27, 2010, at 1:29, Robbie Joosten <[log in to unmask]> wrote:
> Dear Anthony,
>
> That is an excellent question! I believe there are quite a lot of 'rules of thumb' going around. Some of them seem to lead to very dogmatic thinking and have caused (refereeing) trouble for good structures and lack of trouble for bad structures. A lot of them were discussed at the CCP4BB so it may be nice to try to list them all.
>
>
> Rule 1: If Rwork < 20%, you are done.
> Rule 2: If R-free - Rwork > 5%, your structure is wrong.
> Rule 3: At resolution X, the bond length rmsd should be < than Y (What is the rmsd thing people keep talking about?)
> Rule 4: If your resolution is lower than X, you should not use_anisotropic_Bs/riding_hydrogens
> Rule 5: You should not build waters/alternates at resolutions lower than X
> Rule 6: You should do the final refinement with ALL reflections
> Rule 7: No one cares about getting the carbohydrates right
>
>
> Obviously, this list is not complete. I may also have overstated some of the rules to get the discussion going. Any addidtions are welcome.
>
> Cheers,
> Robbie Joosten
> Netherlands Cancer Institute
>
>> Apologies if I have missed a recent relevant thread, but are lists of
>> rules of thumb for model building and refinement?
>>
>>
>>
>>
>>
>> Anthony
>>
>>
>>
>> Anthony Duff Telephone: 02 9717 3493 Mob: 043 189 1076
>>
>>
>>
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