This explains why I cannot reproduce published R-factors (with files from PDB I get ~40%). If I force my favorite refinement program to use P21212 then I get R close to reported in PDB file header. This makes it worth reminding that it's rarely a good idea to edit PDB file out of refinement.
Pavel On Fri, Apr 12, 2013 at 12:33 PM, Phoebe A. Rice <[email protected]> wrote: > Looks like a typo to me: if you change the CRYST space group record from > P212121 to P21212, as the paper says it is, the packing problem goes away. > > ++++++++++++++++++++++++++++++++++++++++++ > > Phoebe A. Rice > Dept. of Biochemistry & Molecular Biology > The University of Chicago > > 773 834 1723; [email protected] > http://bmb.bsd.uchicago.edu/Faculty_and_Research/ > > http://www.rsc.org/shop/books/2008/9780854042722.asp > > ________________________________________ > From: CCP4 bulletin board [[email protected]] on behalf of Michel > Fodje [[email protected]] > Sent: Friday, April 12, 2013 2:17 PM > To: [email protected] > Subject: Re: [ccp4bb] Puzzling Structure > > By the way, you will need to show symmetry atoms to see the problem. > > >-----Original Message----- > >From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of > >Michel Fodje > >Sent: April-12-13 1:14 PM > >To: [email protected] > >Subject: [ccp4bb] Puzzling Structure > > > >Has anyone else noticed a problem with the structure of the N-terminal > >capsid domain of HIV-2 PDB 2wlv. > > > >Load it up to in coot and navigate to residue B118. > > > > > > > >/Michel. >
