Hi Mathias, It does look to me as though the documentation is incorrect. I will see if Dorothee, who knows more, can answer in detail. To encourage everyone to try out the Phenix user chatbot ( https://phenix-online.org/chatbot), I used it to create a work-around for this problem: "can you translate the selection "(chain IN and not (phosphate or ribose)" into one that explicitly lists all the atom types that are to be excluded" It replied with a detailed answer that included a rewrite of your selection that does not use smart selections (you might double check that these are all the right atom names...): chain IN and not (name P or name O1P or name O2P or name O3' or name O5' or name C1' or name C2' or name C3' or name C4' or name C5' or name O4' or name O2') Of course in this particular case it will not answer correctly as to why the original selection did not work if the documentation itself is not correct (the chatbot gets its information from the documentation, papers, and tutorials) All the best, Tom T On Fri, Jul 18, 2025 at 1:00 AM Vorländer,Matthias Kopano < [email protected]> wrote:
Hi everyone,
I am trying to truncate an RNA chain to backbone only using phenix.pdb tools with this command:
phenix.pdbtools input.cif remove="(chain IN and not (phosphate or ribose)"
I get:
AtomSelectionError: RuntimeError: Atom selection syntax error at word "phosphate". Atom selection string leading to error: (chain IN and not (phosphate or ribose)
Based on https://phenix-online.org/documentation/reference/atom_selections.html< https://phenix-online.org/documentation/reference/atom_selections.htmlI> I thought “phosphate” and “ribose” should be valid selection key words, but can’t figure out what I am doing wrong and would appreciate your help : )
Thanks in advance and best wishes, Matthias _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s
-- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: [email protected] Tel: 505-431-0010