 |
 |
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. >