id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3397 ChimeraX: mmcif connectivity lost in some chains; OK in Coot  + PDB ATOM -> HET ATM jacob_r_anderson@… Greg Couch "{{{ Dear ChimeraX Bugs, Thank you very much for your work on this great software. We use it daily, and without which it would be extremely difficult to articulate our science. I am touching base with a problem I am having opeing a mmcif file in chimerax. While trying to avoid this issue, I also ran into another problem when saving a PDB with a two letter chain ID. For context, I am running ChimeraX on Ubuntu 20.04 using a fresh deb install this morning: chimerax --version UCSF ChimeraX version: 1.0 (2020-06-04) © 2016-2020 Regents of the University of California. All rights reserved. To be explicit, both problems are entirely reproducible. Specifically, I have an mmcif file (attached) that when opened in ccpem's or ccp4s Coot v0.9-pre, has all the connectivity present. However, when I switch to ChimeraX, the connectivity of some chains are lost. A good example of this contrast on chain connectivity fidelity is chain LA and LB. (photo attached). Oddly, in this microtubule, all the alpha tubs have connectivity, and beta do not. I tried reading through the ChimeraX documentation on this CIF format, but it remained not totally clear to me what is going awry in some chains but not in others. Secondly, to avoid this connectivity issue, I went to save the model as a PDB instead of an mmcif, with the hope the PDB would maintain connectivity in ChimeraX. I did file conversion in Coot. Reviewing the file, it looks OK. It also opens and docks OK in ChimeraX with proper connectivity. However, upon saving the pdb with its updated coordinates after using the ""Fit To Map"" module, all the atoms have been changed to HETATM (in zip as fit_to_map_PDB_savedinchimerax.pdb). Might this be a bug related to the two letter chain ID of the input PDB? or possibly a product of saving a cif file in coot to pdb? It was reproduced upon a second try and by another member of our laboratory. Since this was a lot, I guess to summarize the two problems are: 1) A mmcif file that opens with proper connectivity in a different software (Coot), does not open with that same connectivity in ChimeraX 2) A PDB file with two letter chain IDs, when saved, converts all ATOM lines to HETATM lines. We would very much appreciate any help regarding these two problems. [cid:868033cd-2f63-4156-863c-ff3ee8685350] _____________________________ Jacob R. Anderson GSAS Chemical Biology | G1 Cell: 440-308-9297 Mail: jacob_r_anderson@hms.harvard.edu }}} [[Image(image.png)]] [attachment:""OK_in_coot.mmcif""] [attachment:""pdb_hetatm_files.zip""] " defect closed normal Input/Output fixed Eric Pettersen all ChimeraX