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
