Working with c-beta truncated models in ISOLDE
Hi everyone, Is there a way to work with c-beta truncated models in ISOLDE? For truncated residues, Isolde brings up the unparameterized residues dialog, and matches as a possible template the ligand “TRUNC_CB”, which seems reasonable. Since the model also contains complete sidechains, I would not want to rebuild all residues to template, and doing it residue-by-residue is impractical, too. Can the “rebuild to template for all residues of this name” be limited to a selection? Thanks a lot, Matthias
Hi Matthias, I guess the "for all residues of this name" label is slightly misleading here - what it's actually supposed to say is "for all residues of this name *that don't already have successful template matches*". In other words, as long as you've already added hydrogens etc. then you should be perfectly safe using that option. A more general comment about truncations like this: ISOLDE's general rule is to support truncated sidechains *as long as *the truncation doesn't pass a branch point or break a ring. For CB truncations, this means everything but proline is supported (for well-considered reasons - truncating a Pro to Ala is, in my opinion, never a good idea since it gives the backbone flexibility that it just shouldn't have). In terms of why the truncations are triggering ISOLDE's unparameterised residues dialog, the most likely reason is they still have the HB1 and HB2 atoms attached. ISOLDE's parameterisations of these just leave a bare carbon at the truncation site - which, conveniently, is how ChimeraX's AddH handles them. So maybe just try deleting and re-adding hydrogens? Best, Tristan On Wed, May 28, 2025 at 11:21 AM Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi everyone,
Is there a way to work with c-beta truncated models in ISOLDE? For truncated residues, Isolde brings up the unparameterized residues dialog, and matches as a possible template the ligand “TRUNC_CB”, which seems reasonable. Since the model also contains complete sidechains, I would not want to rebuild all residues to template, and doing it residue-by-residue is impractical, too. Can the “rebuild to template for all residues of this name” be limited to a selection?
Thanks a lot,
Matthias
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Hi Tristan, Amazing, that solved all my problems and made my life a lot easier, thanks a lot for the quick reply!! Best, Matthias From: Tristan Croll <tcroll@altoslabs.com> Date: Wednesday, May 28, 2025 at 12:33 To: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at> Cc: Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Working with c-beta truncated models in ISOLDE Hi Matthias, I guess the "for all residues of this name" label is slightly misleading here - what it's actually supposed to say is "for all residues of this name that don't already have successful template matches". In other words, as long as you've already added hydrogens etc. then you should be perfectly safe using that option. A more general comment about truncations like this: ISOLDE's general rule is to support truncated sidechains as long as the truncation doesn't pass a branch point or break a ring. For CB truncations, this means everything but proline is supported (for well-considered reasons - truncating a Pro to Ala is, in my opinion, never a good idea since it gives the backbone flexibility that it just shouldn't have). In terms of why the truncations are triggering ISOLDE's unparameterised residues dialog, the most likely reason is they still have the HB1 and HB2 atoms attached. ISOLDE's parameterisations of these just leave a bare carbon at the truncation site - which, conveniently, is how ChimeraX's AddH handles them. So maybe just try deleting and re-adding hydrogens? Best, Tristan On Wed, May 28, 2025 at 11:21 AM Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: Hi everyone, Is there a way to work with c-beta truncated models in ISOLDE? For truncated residues, Isolde brings up the unparameterized residues dialog, and matches as a possible template the ligand “TRUNC_CB”, which seems reasonable. Since the model also contains complete sidechains, I would not want to rebuild all residues to template, and doing it residue-by-residue is impractical, too. Can the “rebuild to template for all residues of this name” be limited to a selection? Thanks a lot, Matthias _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/ Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
participants (2)
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Tristan Croll -
Vorländer,Matthias Kopano