If you know what residues are likely to be involved, then set their occupancies to 0.0 (In coot go to Measures - Residue info - edit occ) then do a few cycles of refinement with that model, and then see if there is difference density for those residues...
Quicker than an omit map procedure. Eleanor On 29 April 2015 at 12:16, Aleksandar Bijelic < aleksandar.bije...@univie.ac.at> wrote: > Dear CCP4 users, > > I am currently solving a structure (2.8-2.9 A resolution) of a protein > complexed with a ligand using MR with the apo-form of this protein as model > (resolution of the model is 2.4). After MR-phasing I performed a regular > autobuild run giving me good outputs and thus I refined the best pdb > leading to good values according to R-values and geometry, however, the > denstiy doesn´t look well (but I think it´s due to the moderate > resolution). Now I want to get sure if the side chains which are involved > in the ligand binding are correctly positioned. However, the active site is > suspicously similar to the active site of the model (apo-form) and so I am > afraid that this could be due to model bias. My question is how to check > and to get rid of the bias (if present) at this stage (after several > refinements). I read the publication of Terwilliger about iterative-build > OMIT maps but since I am a bloody novice in this field I didn´t really > understand it. I originally thought iterative-build OMIT maps are performed > to compare the output map with one´s map in order to detect uncertainties, > but what to do next? Or should I start from the beginning but how to > proceed than, what should I do (I am using Phenix via GUI) ... Is it > possible and reasonable to run autobuild with iterative omit map option? Or > is it only reasonable if experimental phases are available? I didn´t run > iterative-build OMIT maps yet because I am not sure how to run it correctly > (what method is the best?) and at my institute the run will take more than > 1 day and I don´t want to block one computer until I am not sure if it is > reasonable. I hope you can give me some advice and help me. Thank you in > advance. > > Regards, > > Aleks > > -- > ------------------------------------------- > Aleksandar Bijelic, MSc. > > Institut für Biophysikalische Chemie > Universität Wien > Althanstrasse 14 > A-1090 Wien > > Tel: +43 1 4277 52536 > e-Mail: aleksandar.bije...@univie.ac.at > > -------------------------------------------- >
