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.
