Dear Inbal, Your observations, plus more of my own, show that we have discovered a bug in Chime that I did not know about: It appears (see below) that when MODEL/ENDMDL records are used, Chime fails to obey CONECT records. I have not come up with a solution in Chime. I am quite sure that MDL will not fix this bug even if we ask them. But this is why many people, especially Miguel Howard, have spent so much time on jmol! (www.jmol.org) jmol should be able to do exactly what you want -- and if not (or if there are bugs) someone (probably Miguel) will fix them! (In addition, it will work on linux and native OSX/Safari as well as all Chime-compatible browsers.) So I think if you switch to jmol, you can acheive your goals. Chime also supports XYZ format for multiple models, and (unlike NMR-PDB format, has built-in support for animation). XYZ format is appropriate for small/inorganic molecules but not for proteins or nucleic acids (because it has no way to specify the position of an element in a group (e.g. CA = Carbon Alpha in PDB format) nor the group to which an atom belongs (so no amino acids nor nucleotides). I have no experience with XYZ format so I cannot tell you if you can get the bond display you want in Chime with XYZ. Here are my observations in Chime: Your model of sulfur hexafluoride specifies six S-F bonds but no F-F bonds. By default, with your two model file, Chime shows the unwanted F-F bonds. When a single model is extracted from your 2-model PDB file (WITHOUT MODEL/ENDMDL records) Chime behaves correctly. By default, it shows only the S-F bonds. This is because, when the number of bonds specified in CONECT records is equal to or greater than (number of ATOMs + number of HETATMs - number of chains), Chime goes automatically into "set connect false" mode, showing only the bonds specified by CONECT records, not the bonds Chime normally calculates for proteins based on interatomic distances. This is all documented at http://www.umass.edu/microbio/rasmol/rasbonds.htm (Removing a single CONECT record correctly makes Chime default to showing the F-F bonds; entering "set connect false" before loading correctly makes Chime show only the 5 remaining S-F bonds.) However, when the single model is enclosed between MODEL 1/ENDMDL records (still only one model present) Chime shows the unwanted F-F bonds (so is failing to go into "set connect false" mode). Further, if you issue an explicit "set connect false" command before loading the model, NO bonds are shown. This is a second bug -- failure to process CONECT records when even a single MODEL record is present. The same behavior is seen with your original 2-model PDB file. The only possible workaround I thought of was to load the model with "load nmrpdb filename.pdb" but that failed to correct either problem. Sincerely, -Eric /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://www.umass.edu/molvis/martz Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop Biochem Structure Tutorials http://MolviZ.org World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List (molvis-list): http://bioinformatics.org/mailman/listinfo/molvis-list - - - - - - - - - - - - - - - - - - - - - - - - - - - */