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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 <[log in to unmask]> 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: [log in to unmask] [mailto:[log in to unmask]] 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 <[log in to unmask]> 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