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 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/
