Re: [ccp4bb] Residue positional validation

[Boaz Shaanan]

Would it not be a good idea to include EDSTATS in ccp4i? I couldn't find it there.          Boaz     Boaz Shaanan, Ph.D.                                         Dept. of Life Sciences                                      Ben-Gurion University of the Negev                          Beer-Sheva 84105                                            Israel                                                                                                                  E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220  Skype: boaz.shaanan                  Fax:   972-8-647-2992 or 972-8-646-1710                          From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson [eleanor.dod...@york.ac.uk] Sent: Tuesday, April 28, 2015 3:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Residue positional validation Or use edstats in CCP4 - gives lots of statistics and a good evaluation of fit Eleanor On 27 April 2015 at 16:26, <Gurusaran Manickam> <satnam...@gmail.com> wrote: Dear Monica, We can also, perhaps, most helpfully quote from our forthcoming article in J Appl Cryst, Volume 48, Part 3 (June 2015):- "An online computing server, Online_DPI, is created and maintained to calculate the ‘Cruickshank DPI’ value for a given three-dimensional protein or macromolecular structure. Also, it estimates the atomic coordinate error for all the atoms available in the structure. It is an easy-to-use web server that enables the users to visualize the computed values dynamically on the client machine. The users can provide the PDB-identification code or upload the three-dimensional atomic coordinates from the client machine. The computed DPI value for the structure and its atomic coordinate errors for all the atoms are included in the revised PDB file." So you can see directly for any specific atom movement, whether it is significant at e.g. the 3 sigma level. So, you don't need to use the average over all the atoms DPI error value, but the atom you are especially interested in. Best wishes, Guru