Hi Debashis, you have "Density fit analysis" in the "Validate" menu in Coot, if it's just that what you're looking for. Ciao, S
On Oct 31, 2013, at 4:43 PM, Debasish Chattopadhyay <[email protected]> wrote: > > Yes, there remains many questions beyond Adit. > I do want to emphasize that the new scrutiny in PDB is very good since it now > includes a density fitting analysis (everything in the structure should be > the density, right) etc. But one has to go through the submission to > generate the report and then has to resubmit the coordinates again if > corrections are necessary. > We know about Molprobity, structures with good Molprobity score and clash > score can still have some issues. > I just saw the note from Pavel and I need to check the option in Phenix. > > Thanks all. > > Debasish > > From: [email protected] [mailto:[email protected]] On > Behalf Of Mahesh Lingaraju > Sent: Thursday, October 31, 2013 10:32 AM > To: Debasish Chattopadhyay > Subject: Re: [ccp4bb] PDB structure validation > > Hi > > One can do an unofficial validation in Adit server ( one of the pdb > deposition services) but i have found that although it is almost the same > thing, it does not provide a lot of information that we get from the official > report. > > I found that the apps from the PDB_redo help a lot in ironing out the kinks > at the final stages of structure refinement that are otherwise not so > obvious. > > Thanks > > Mahesh > > > > > On Thu, Oct 31, 2013 at 11:25 AM, Debasish Chattopadhyay <[email protected]> > wrote: > I was wondering if there is a way to generate a PDB validation report before > depositing the coordinates so that one can go back and make necessary > corrections to the file before deposition. It will save a lot time and > perhaps would improve the quality of deposited structures. > > Debasish Chattopadhyay > > University of Alabama at Birmingham > CBSE-250 > 1025 18th Street South, Birmingham, Al-35294 > USA > Ph: (205)934-0124; Fax: (205)934-0480 > -- Sebastiano Pasqualato, PhD Crystallography Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 web http://is.gd/IEO_xtalU
