> On Thursday 16 March 2006 20:37, Egon Willighagen wrote: >> how well does mmCIF reading work? Anyone who uses this on a large set of >> data? Ever encountered trouble? Is it save to be used for reading >> structures from pdb.org? > > I found a few 'issues' with Jmol's current mmCIF reader with respect to > the > mmCIF docs on pdb.org (using 4HHB only yet): > > - HETATOM is neglected, so 'select ligand' is not working
HETATM is supported in some ways ... look at 1A00.cif The hemes are HETATMs that get recognized by Jmol. > - Jmol's reader uses '_atom_site.b_iso_or_equiv' but the pdb.org mmCIF > uses '_atom_site.B_iso_or_equiv' > - and, similarly, Jmol: '_atom_site_label_atom_id' vs. pdb.org > '_atom_site.label_atom_id ' > > The latter two seem to be the same using the CifReader's isMatch() method. Correct. As I recall, isMatch was put in place to deal with case sensitivity issues and whether or not a leading _ was present. (Users wanting opinions about the CIF standard can search the archives). > But the first is a problem I think. Will write and commit > a patch for that now. OK. But first you should understand how this case differs from 1A00.cif ... where we have HOH and heme HETATMs. Miguel ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid0944&bid$1720&dat1642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
