Lijun The definition: https://mmcif.wwpdb.org/dictionaries/mmcif_ma.dic/Items/_cell.Z_PDB.html says it is not mandatory and only for compatibility.
We don't output this so it seems that Coot may need to allow for its absence. I have not received a response from Paul Emsley about this from my email to him but I thought the community might like to know. Cheers Nigel --- Nigel W. Moriarty Building 91, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : nwmoria...@lbl.gov Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464 On Mon, Apr 21, 2025 at 12:40 PM Nigel Moriarty <nwmoria...@lbl.gov> wrote: > Lijun > > Would you mind sending me the files? > > BTW, there are several ways to get help from Phenix here. > https://phenix-online.org/help > > Cheers > > Nigel > > --- > Nigel W. Moriarty > Building 91, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > Berkeley, CA 94720-8235 > Email : nwmoria...@lbl.gov > Web : CCI.LBL.gov > ORCID : orcid.org/0000-0001-8857-9464 > > > On Fri, Apr 18, 2025 at 11:49 AM Lijun Liu <lijunli...@gmail.com> wrote: > >> Hi: >> >> First of all: I am not sure if it is a coot problem or a phenix problem? >> >> I am using coot version of 0.9.8.95. When I read some .cif coordinate >> files, it gave error like below: >> >> ============================== >> >> INFO:: Reading coordinate file: KlaeA_1011.cif >> ERROR:: failed to get cell >> INFO:: There was an error reading KlaeA_1011.cif. >> INFO:: read error 23 READ: Expected data field not found. >> CIF ITEM: structure _cell.z_pdb data [NULL] >> >> ============================== >> >> I had some .cif files output from the same version of phenix.refine, but >> they were loading without any problems. I checked the head section of >> SYMM and CELLS of those files, all looked like normal, same style of >> lines with different values only. These .cif files, no matter working >> or not, did not contain strings "_cell.z_" in file. >> >> Launching coot firstly and then trying loading those .cif file from >> file/open-coordinates menu, not working either. >> >> I checked around, other users also had the similar problems. >> >> Also, no problems when loading the REFMAC .mmcif files, with a few tests. >> >> Thanks for suggestions. >> >> Lijun >> >> ######################################################################## >> >> 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/ >> > ######################################################################## 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/
