Syntax help: phenix.pdb_tools to remove selected bases from file

Vorländer,Matthias Kopano

18 Jul 2025 18 Jul '25

6:59 a.m.

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

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Tom Terwilliger

18 Jul 18 Jul

3:10 p.m.

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

Vorländer,Matthias Kopano

3:58 p.m.

Hi Tom, Thanks for the reply! I am a fan of the chatbot and used it to get to the phosphate and ribose syntax. I also got initial reply containing explicit atom names, but that seemed less robust to me (i.e if you have modified bases this would fail). Indeed the chatbot syntax solution with explicit atom names led to stray atoms floating in space. I was therefore hoping that the in-built classification would work as a more robust solution. Best wishes, Matthias From: Tom Terwilliger Date: Friday, July 18, 2025 at 17:39 To: Vorländer,Matthias Kopano Cc: [email protected] , Tom Terwilliger Subject: Re: [phenixbb] Syntax help: phenix.pdb_tools to remove selected bases from file 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 mailto:[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]mailto:[email protected] To unsubscribe send an email to [email protected]mailto:[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]mailto:[email protected] Tel: 505-431-0010

Oleg Sobolev

4:26 p.m.

Hi Matthias, Tom, Indeed, the documentation seems to be slightly off for this particular selection keywords for pdbtools. Originally, none of the "smart" selections were available in pdbtools, but quite some time ago we implemented some of them, like protein, nucleotide, water, within, residues_within. Unfortunately, phosphate and ribose were not one of those. As for modified bases with non-standard atom names, even smart selections available in presence of restraint information won't be helpful. They are implemented as explicit lists of atom names. So you'll end up listing non-standard atom names anyway. Best regards, Oleg Sobolev. On Fri, Jul 18, 2025 at 8:58 AM Vorländer,Matthias Kopano < [email protected]> wrote:

...

Hi Tom,

Thanks for the reply!

I am a fan of the chatbot and used it to get to the phosphate and ribose syntax. I also got initial reply containing explicit atom names, but that seemed less robust to me (i.e if you have modified bases this would fail). Indeed the chatbot syntax solution with explicit atom names led to stray atoms floating in space. I was therefore hoping that the in-built classification would work as a more robust solution.

Best wishes, Matthias

From: Tom Terwilliger Date: Friday, July 18, 2025 at 17:39 To: Vorländer,Matthias Kopano Cc: [email protected] , Tom Terwilliger Subject: Re: [phenixbb] Syntax help: phenix.pdb_tools to remove selected bases from file 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]mailto:[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

_______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s

Jorge Iulek

21 Jul 21 Jul

4:26 p.m.

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

Tom Terwilliger

4:49 p.m.

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 wrote:

...

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

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

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Jorge Iulek
Oleg Sobolev
Tom Terwilliger
Vorländer,Matthias Kopano