Isolde error: no rotamers

[dgutierrez@…]

Hello,


I keep getting this error when I try to run Isolde. This is after initializing in the isolde gui. Sorry if this a mistake on my part, I am using chimeraX and Isolde for the first time. Also, under "map setting dialogue" I cannot scroll through any maps.


Exception: ILE: None

File "/Users/DG/Library/Application Support/ChimeraX/0.5/site-packages/chimerax/isolde/isolde.py", line 2161, in _prepare_all_interactive_restraints
raise Exception('{}: {}'.format(r.residue.name, r.dihedrals))

See log for complete Python traceback.

If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and describe what you were doing and include a copy of the contents of the log. Don't include any data you wish to remain private since a publicly viewable bug report will be created.


Best,

Dominique Gutierrez

[Eric Pettersen]

Reported by Dominique Gutierrez

[Tristan Croll]

Hi Dominique,

That (not really clear, I admit) error message is telling you that an ILE residue either (a) is missing atoms, or (b) has mis-named atoms. Like essentially any other MD-based method, ISOLDE requires you to have all residues complete with all atoms (including hydrogens), and the atoms must be named according to PDB standard. If you're using a model that you've previously simulated using CHARMM (or, for example, NAMD using the CHARMM forcefield), that may also be the culprit. CHARMM has a few annoying naming idiosyncrasies, including naming the CD1 atom of ILE "CD". If you feel comfortable with sending me a copy of your coordinates (direct to my email, not to the list) I'd be happy to help prepare them for ISOLDE.

Regarding your query about maps: at present ISOLDE does not work directly with real-space maps (that is, ChimeraX Volume objects), but requires reciprocal-space reflection data in MTZ format. If you're working with a real-space EM map, you can convert it quite straightforwardly using phenix.map_to_structure_factors (see ​http://phenix-online.org/).

You might find my tutorial video at ​https://www.youtube.com/watch?v=limaUsNAVL8 useful to get a better idea of the ISOLDE workflow.

[Tristan Croll]

Will continue any further discussion off-list.