Hi Jorge,
Oh yes, the parentheses do have to match. That string would yield an error
whether phosphate and ribose are recognized or not.
All the best,
Tom T
On Mon, Jul 21, 2025 at 10:27 AM Jorge Iulek
Dear Matthias,
Two ' ( ( ' and one ' )' in
phenix.pdbtools input.cif remove="(chain IN and not (phosphate or ribose)"
is inoffensive - - it seems ?
Jorge
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
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-- 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