First Q.
Checking the refined structure in detail..
This is personal.
Basic - run REFMAC with monitor many - that lists really bad bonds,
chirality, symmetry clashes etc, but frankly by the time you are at
R=20% there shouldnt be many of those..
You need to be sure you have described any CIS peptides correctly -
conflict can arise between REFMAC and COOT over whether something is or
is not a CISPEP..
Then I use the COOT validation tools as a first and excellent start.
Missing blobs, Difference map peaks
Correct GLN/ASN etc.
Look at ramachandran outliers - etc etc
MOLPROBITY is great at the end - I think it results in overkill if you
still have any gross errors to correct..
Q2.
Kevin cowtan has written a wonderful utility called csymmatch. It moves
a seciond solution to the same origin and symmetry operator as the first
csymmatch -pdbin-ref oldone.pdb -pdbin newone.pdb
-pdbout newone-shifted -origin-hand
It is a great help after MR or automated model building..
You still have to match the chain IDs if you want A1 to match A2 etc,
but it is a great help..
Eleanor
On 06/09/2011 08:46 AM, Ting-Wei Jiang wrote:
> Dear experts,
> I got two questions regarding refinement and structure determination by MR.
>
> 1.I got a dataset of resolution at 2A refined to Rvalue~20% and Rfree~24%
> I want to know if there is any program in CCP4 could help me to check the
> refined structure in detail.
> For example,the model statistics in CNS could list some information that
> infer band,angle violation...etc
> Or I should ask what do I need to check before submitting to PDB.
>
> 2.A dataset of resolution collected to 2.2A is from native protein
> crystal(A) and its complex form(A'+B)
> whose PDB code is 2QN5 was already determined by MR(use another protein as
> search model).I planned
> to use A' as search model but the A' looks broken.
> This number of molecules in AU was predicted to 4~6 using Mathews
> coefficient.
> N/a M.C. solvent%
> 4 2.99 58.92
> 5 2.39 48.65
> 6 1.99 38.38
> The coordinate or orientation of output pdb(as attached figure) from MR
> are always different since I changed
> parameter,such as different resolution,Multi copy,search mode...etc. even
> the contrast value of every run
> is pretty high(>>3)
> I really don't what happened with this dataset and any suggestion would be
> greatly appreciated.
>
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