The JCSG validation server is useful – it will run ADIT check, MolProbity, real space CC, etc.
http://smb.slac.stanford.edu/jcsg/QC/ On Thu, Oct 31, 2013 at 2:22 PM, rjguan <[email protected]> wrote: > ** > 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 <[email protected]> > *Date:* 2013-10-31 11:48 > *To:* CCP4BB <[email protected]> > *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 > > > > >
