we have a PSVS server, and welcome people to try and give back comments: http://psvs-1_5-dev.nesg.org/
Rongjin Guan From: Bosch, Juergen Date: 2013-10-31 11:48 To: CCP4BB Subject: Re: [ccp4bb] PDB structure validation You do use Coot and look at the density plots right ? Phenix will essentially do the same but in text form (unless you use the GUI). You can also do this with Solve/Resolve and you can write your own script with CCP4 available tools to do the same RSR fit diagram. Jürgen On Oct 31, 2013, at 11:43 AM, Debasish Chattopadhyay 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 ...................... Jürgen Bosch Johns Hopkins University Bloomberg School of Public Health Department of Biochemistry & Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Office: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-2926 http://lupo.jhsph.edu
