Hari I'm happy to take a closer look if you send me the files directly.
Phenix has an omit map known as the Polder map that takes care of the solvent masking. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : nwmoria...@lbl.gov Fax : 510-486-5909 Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 On Wed, Apr 7, 2021 at 7:49 AM Bernhard Rupp <hofkristall...@gmail.com> wrote: > > 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> 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> *On Behalf Of *Hari > shankar > *Sent:* Wednesday, April 7, 2021 08:47 > *To:* 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&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 > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&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 > > kostr...@genzentrum.lmu.de > > WWW: 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&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 > ######################################################################## 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/
