Dear Roberto, I believe there are many "badly modeled" ligands with distorted geometry deposited in the PDB. Basically, because they haven't been checked properly beforehand, so I think running a geometry check of you desired ligand against the PDB.
I think running your modeled geometry against the CSD would flag up easily issues. MOGUL http://www.ccdc.cam.ac.uk/products/csd_system/mogul/ has been a great tool, which can be easily incorporated into COOT (ouuups). :) Cheers Stefan -----Ursprüngliche Nachricht----- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Robert Immormino Gesendet: Donnerstag, 10. März 2011 21:56 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Can procheck or other tools report bad geometry for ligand? Hi Halliang, If the ligands are in the pdb het dictionary I think MolProbity will look at bonds and angles...maybe even dihedrals. Cheers, -bob On Thu, Mar 10, 2011 at 12:23 PM, Hailiang Zhang <zhan...@umbc.edu> wrote: > Hi there, > > I want to found some bad geometry for my ligand (sugar rings). The > procheck .out file seems only shows the bad bond length or angles for > protein. Is there any way we can get these information for sugar rings? > > Thanks in advance! > > Hailiang >
