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 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/
