On the "Ligand" tab (upper left of web page), at left you'll see "PDB (model coordinates)" and "PDB (ideal coordinates)". The Ideal coords really are idealized, including a very different torsion between the two ring systems in this ligand. The Model coords seem correct (one of the two in the asymmetric unit was chosen, on some basis), but, again a "Hmm?", the Bfactors of the Model coords were all reset to 10.00. Dave
> -----Original Message----- > From: Artem Evdokimov [mailto:[EMAIL PROTECTED] > Sent: Tuesday, December 09, 2008 9:36 PM > To: Borhani, David; CCP4BB@JISCMAIL.AC.UK > Subject: RE: [ccp4bb] Summary - torsion angle restraints in REFMAC > > Interestingly, in the interactive 3D applet view of the > ligand from the PDB > the two are perfectly in plane, whereas in the protein viewer > the two groups > are clearly out of plane. I assume that this means that the > coordinates for > the 3D ligand view are re-computed internally and are not > representative of > what's actually in the PDB. > > Hmm? > > Artem > > -----Original Message----- > From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of > Borhani, David > Sent: Tuesday, December 09, 2008 9:25 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Summary - torsion angle restraints in REFMAC > > RE: Ian's and Eckhard's wise suggestion to deposit non-standard > parameters used to refine ligands: > > I have had some ligands where the 1 & 8 peri-substituents (amino & > methyl groups) on a 6/6 fused aromatic ring (deazapteridine > derivatives) > were very clearly out of the plane. It took extensive > fiddling with the > refmac dictionary to get the torsion & planarity restraints relaxed > enough so that these two atoms were allowed to move into the > very clear > difference density waiting for them, even with 1.1 A data! > > See http://www.rcsb.org/pdb/explore.do?structureId=1KMS and > http://www.rcsb.org/pdb/explore.do?structureId=1KMV for > examples; paper > is here: http://www.ncbi.nlm.nih.gov/pubmed/12096917 > > I thought I had deposited the refmac library file, but now I > cannot find > it on the PDB web site. Maybe I'm not looking in the right > place, but if > you click, in the ligand (LII) area, on ligand structure "view", then > (at left) "Component definition (CIF)", you can find this: > http://www.rcsb.org/pdb/files/ligand/LII.cif. BUT, THIS IS > NOT MY FILE! > Rather, some auto-generated file (probably wrong; definitely doesn't > have my relaxed parameters). > > Similarly, for http://www.rcsb.org/pdb/explore.do?structureId=2C2S > (http://www.ncbi.nlm.nih.gov/pubmed/17569517), with a rather strange > carborane ligand, I *distinctly* remember depositing the library file, > because the EBI deposition software got completely tied in > knots trying > to interpret the deposited coords. Again, no files to be found on the > PDB. http://www.rcsb.org/pdb/files/ligand/34B.cif is again > not my file, > but an auto-generated one (probably wrong, given the trouble > the EBI s/w > had). > > Hoping some folks at EBI/RCSB monitor the CCP4BB, > > Dave > David Borhani, Ph.D. > D. E. Shaw Research, LLC > 120 West Forty-Fifth Street, 39th Floor > New York, NY 10036 > [EMAIL PROTECTED] > 212-478-0698 > http://www.deshawresearch.com > >
