Re: [ccp4bb] Composit omit map vs. ligand

Dear Pavel, Thank you for your reply. I would have thought that many of your users in the drug discovery field would have been aware of it, as many of them use both Phenix and BUSTER. An even more explicit and detailed description of that feature, dated March 2011, may be found at

Re: [ccp4bb] Composit omit map vs. ligand

Dear Gerard, Thank you so much for letting us know of the reference and details about your long-standing BUSTER method for ligand density maps which we now see is very similar to our recent polder map method. We apologize for not being aware of the early reference and we will be very sure to cite

Re: [ccp4bb] Composit omit map vs. ligand

Dear Pavel, As much as I would have wished to, I was unable to contribute to this thread for the past week because of more pressing matters. I hope it hasn't entirely gone cold in the minds of CCP4BB readers. I want to congratulate the Phenix developers for having come up with such a ca

Re: [ccp4bb] Composit omit map vs. ligand

And here is an excellent Polder tutorial https://www.youtube.com/watch?v=TcTuMJayh5c you can watch on YouTube in the Phenix Tutorials channel Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 9

Re: [ccp4bb] Composit omit map vs. ligand

In addition to excellent Kay's reply.. Also make sure to check refined B factors. Note, if the ligand is not there then that volume is likely filled with bulk-solvent. Now low occupancy in combination with very large B factors may approximate bulk-solvent quite well. The Polder map along with thre

Re: [ccp4bb] Composit omit map vs. ligand

Dear colleagues, First of all, I would like to thank to all who responded! I have selected some answers and my reactions to sum up: 1) Kay Diedrichs - try a Polder map: clear density for the ligand at 3 sigma appeared. 2) JR Helliwell - build first five atoms and check the density now (read

Re: [ccp4bb] AW: [ccp4bb] Composit omit map vs. ligand

; 1.5 to 2-sigma level I would not worry too much. > > Best, > Herman > > > -Ursprüngliche Nachricht- > Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von > Kay Diederichs > Gesendet: Mittwoch, 8. Februar 2017 11:43 > An: CCP4BB@JISCMAI

[ccp4bb] AW: [ccp4bb] Composit omit map vs. ligand

Diederichs Gesendet: Mittwoch, 8. Februar 2017 11:43 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Composit omit map vs. ligand Dear Petr, if I understand correcty, the mFo-DFc density (1) shows almost nothing, but the 2mFo-DFc (2) as well as the composite omit map (3) show the ligand? As you say

Re: [ccp4bb] Composit omit map vs. ligand

Dear Petr, if I understand correcty, the mFo-DFc density (1) shows almost nothing, but the 2mFo-DFc (2) as well as the composite omit map (3) show the ligand? As you say, the apparent contradiction between (1) versus (2)&(3) is unexpected. One explanation could be that the Fc are simply too b

[ccp4bb] Composit omit map vs. ligand

Dear colleagues, we have a dataset with potential enzyme:ligand complex at 2.2 AA resolution. The ligand is very good substrate for the enzyme, we used soaking. We do not see the ligand in the regular difference electron density, only five out of twenty atoms. However, the ligand placed at th