> setting occupancies of omitted atoms to zero has the danger of leaving a hole
Not quite. We probably need Garib to confirm this, but I tried this many times, and if in refmac the occupancy is really zero (0.00), then this does not happen, and the ligand is treated as not present. An occupancy of 0.02 however, already suffices to have the solvent excluded and the fo component from the solvent shows up nicely. The effect is indeed dramatic, cf. Figure 2 (and F1 for more fun with the same ligand) https://febs.onlinelibrary.wiley.com/doi/epdf/10.1111/febs.14320 Best, BR From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Dirk Kostrewa Sent: Wednesday, April 7, 2021 03:59 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Omit maps in phenix and ccp4 Dear Eleanor, setting occupancies of omitted atoms to zero has the danger of leaving a hole with the shape of these atoms in the bulk solvent mask, leading to positive difference density just because of the missing bulk solvent density. Since the days of X-PLOR, I always removed the omitted atoms. I never tried this with REFMAC5, though. Cheers, Dirk. On 07.04.21 11:46, Eleanor Dodson wrote: Well - I use COOT for this sort of task, and dont trust the automated tools. my procedure is load COOT - probably after a refinement cycle set occupancy of ligand(s) to 0.00 ( Measures - residue information - change occupancy) Look at the environment critically . eg if an ARG or other bulky side chain nearby , or waters etc selectively set occupancies to 0.00 Doo some more cycles of refinement with this coordinate set to remove any memory of the ligand. Look at the map - if the ligand and other zero occ atoms is still in the right place reinstate them, or try to reinterpret density.. Eleanor On Wed, 7 Apr 2021 at 08:39, Bjarte Aarmo Lund <bjarte.l...@uit.no <mailto:bjarte.l...@uit.no> > wrote: Dear Hari, With regards to 1) Is 15 the number of atoms in your molecule? Or is it the number of hydrogens? The CIF file may have the wrong residue name or lack the hydrogens depending on how you built the ligand-protein complex. There is also a phenixbb for phenix questions, http://www.phenix-online.org/mailman/listinfo/phenixbb Kind regards, Bjarte Aarmo Lund Postdoc UiT The Arctic University of Norway From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > On Behalf Of Hari shankar Sent: Wednesday, April 7, 2021 08:47 To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Omit maps in phenix and ccp4 Dear All, I have a ligand-protein complex and I wish to calculate different kinds of omit maps (say, composite omit maps, simulated annealing maps, other unbiased fo-fc maps ). I wish to omit the ligand and 3.5 angstrom 3D space around it. I have tried phenix for this purpose but get this error message consistently. "Fatal problems interpreting model file: no of atoms with unknown nonbonded energy type symbols: 15 Please edit the model file to resolve the problems and/of supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary." This error occurs despite supplying the CIF file for the ligand. I have tried to remake the CIF/PDB files from SMILES strings, by drawing the molecule in both ccp4 (acedrug) as well as phenix (elBOW and Readyset go). Nothing seems to work. 1. Is there something I have missed out that can solve this issue? 2. Is there a program in CCP4i that can be used to generate the required omit maps? 3. In general, how do I omit 3.5 ang of the space around the ligand during this map calculations? Thank you so much for your time. Hari _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> &A=1 _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> &A=1 _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> &A=1 -- ******************************************************* Dirk Kostrewa Gene Center Munich Department of Biochemistry, AG Hopfner Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone: +49-89-2180-76845 Fax: +49-89-2180-76998 E-mail: dirk.kostr...@lmu.de <mailto:dirk.kostr...@lmu.de> kostr...@genzentrum.lmu.de <mailto:kostr...@genzentrum.lmu.de> WWW: www.genzentrum.lmu.de <http://www.genzentrum.lmu.de> ******************************************************* _____ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> &A=1 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
