ISOLDE and secondary structure restraints
Hi all,
I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess:
Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script?
Cheers, Guido
Not the hard-coded helix and beta-sheet restraints, I’m afraid. But you can get a very similar (probably better, TBH) result with something like:
isolde restrain distances #1&(helix|strand)&backbone isolde restrain torsions #1&(helix|strand) sidechain false
The advantage of those is that (a) they’ll work a bit better when the true conformation isn’t *perfect* helix or strand, and (b) they have a lot more flexibility in terms of your ability to fine-tune their behaviour (for models fetched from the Alphafold DB, try adding the argument “adjustForConfidence true” to automatically take the pLDDT and PAE values into account).
— Tristan
On 13 Mar 2022, at 14:42, Guido Hansen via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi all,
I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess:
Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script?
Cheers, Guido
--
PD Dr. Guido Hansen Group Leader
[Uni-Lübeck] Universität zu Lübeck Institut für Biochemie Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen@biochem.uni-luebeck.demailto:hansen@biochem.uni-luebeck.de www.biochem.uni-luebeck.dehttp://www.biochem.uni-luebeck.de Ratzeburger Allee 160 23562 Lübeck
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks for your suggestions. However, I think that when applying distance restraints using the command below also distances of mainchain atoms of secondary structure elements to nearby sidechain atoms get restrainted.
isolde restrain distances #1&(helix|strand)&backbone
What you get when using the gui is something like that:
-- Guido
Am 13.03.2022 um 16:07 schrieb Tristan Croll:
Not the hard-coded helix and beta-sheet restraints, I’m afraid. But you can get a very similar (probably better, TBH) result with something like:
isolde restrain distances #1&(helix|strand)&backbone isolde restrain torsions #1&(helix|strand) sidechain false
The advantage of those is that (a) they’ll work a bit better when the true conformation isn’t *perfect* helix or strand, and (b) they have a lot more flexibility in terms of your ability to fine-tune their behaviour (for models fetched from the Alphafold DB, try adding the argument “adjustForConfidence true” to automatically take the pLDDT and PAE values into account).
— Tristan
On 13 Mar 2022, at 14:42, Guido Hansen via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi all,
I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess:
Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script?
Cheers, Guido
--
*PD Dr. Guido Hansen *Group Leader
Uni-Lübeck
*Universität zu Lübeck* *Institut für Biochemie*
Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen@biochem.uni-luebeck.de www.biochem.uni-luebeck.de
Ratzeburger Allee 160 23562 Lübeck
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Oops! My bad - was responding on the move, and forgetting my own implementation. You're right, the "isolde restrain distances" command works on a per-residue basis, so sidechain atoms will be included regardless. On the other hand, the "isolde release distances" command works per-atom, so after the restrain command you can selectively release the sidechain restraints with:
isolde release distances #1&sideonly ________________________________ From: Guido Hansen hansen@biochem.uni-luebeck.de Sent: 15 March 2022 16:20 To: Tristan Croll tic20@cam.ac.uk Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] ISOLDE and secondary structure restraints
Thanks for your suggestions. However, I think that when applying distance restraints using the command below also distances of mainchain atoms of secondary structure elements to nearby sidechain atoms get restrainted.
isolde restrain distances #1&(helix|strand)&backbone
[cid:part1.09p0uiHA.41fj6uxZ@biochem.uni-luebeck.de]
What you get when using the gui is something like that:
[cid:part2.0mNP8JTc.JBo6Z60y@biochem.uni-luebeck.de]
-- Guido
Am 13.03.2022 um 16:07 schrieb Tristan Croll: Not the hard-coded helix and beta-sheet restraints, I’m afraid. But you can get a very similar (probably better, TBH) result with something like:
isolde restrain distances #1&(helix|strand)&backbone isolde restrain torsions #1&(helix|strand) sidechain false
The advantage of those is that (a) they’ll work a bit better when the true conformation isn’t *perfect* helix or strand, and (b) they have a lot more flexibility in terms of your ability to fine-tune their behaviour (for models fetched from the Alphafold DB, try adding the argument “adjustForConfidence true” to automatically take the pLDDT and PAE values into account).
— Tristan
On 13 Mar 2022, at 14:42, Guido Hansen via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi all,
I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess:
Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script?
Cheers, Guido
--
PD Dr. Guido Hansen Group Leader
[Uni-Lübeck]
Universität zu Lübeck Institut für Biochemie
Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen@biochem.uni-luebeck.demailto:hansen@biochem.uni-luebeck.de www.biochem.uni-luebeck.dehttp://www.biochem.uni-luebeck.de
Ratzeburger Allee 160 23562 Lübeck
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users --
PD Dr. Guido Hansen Group Leader
[Uni-Lübeck]
Universität zu Lübeck Institut für Biochemie
Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen@biochem.uni-luebeck.demailto:hansen@biochem.uni-luebeck.de www.biochem.uni-luebeck.dehttp://www.biochem.uni-luebeck.de
Ratzeburger Allee 160 23562 Lübeck
Hi,
I would like to pick up this old thread. Do I interpret this correctly that ISOLDE ignores the secondary structure annotations in the PDB header and has its own way of calculating what’s a helix and a strand? If so, are these definitions written in the PDB header when the file is saved, or is there an option to do so?
Many thanks, Matthias
From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Tristan Croll via ChimeraX-users chimerax-users@cgl.ucsf.edu Date: Tuesday, 15. March 2022 at 17:30 To: Guido Hansen hansen@biochem.uni-luebeck.de Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] ISOLDE and secondary structure restraints Oops! My bad - was responding on the move, and forgetting my own implementation. You're right, the "isolde restrain distances" command works on a per-residue basis, so sidechain atoms will be included regardless. On the other hand, the "isolde release distances" command works per-atom, so after the restrain command you can selectively release the sidechain restraints with:
isolde release distances #1&sideonly ________________________________ From: Guido Hansen hansen@biochem.uni-luebeck.de Sent: 15 March 2022 16:20 To: Tristan Croll tic20@cam.ac.uk Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] ISOLDE and secondary structure restraints
Thanks for your suggestions. However, I think that when applying distance restraints using the command below also distances of mainchain atoms of secondary structure elements to nearby sidechain atoms get restrainted.
isolde restrain distances #1&(helix|strand)&backbone
[cid:part1.09p0uiHA.41fj6uxZ@biochem.uni-luebeck.de]
What you get when using the gui is something like that:
[cid:part2.0mNP8JTc.JBo6Z60y@biochem.uni-luebeck.de]
-- Guido
Am 13.03.2022 um 16:07 schrieb Tristan Croll: Not the hard-coded helix and beta-sheet restraints, I’m afraid. But you can get a very similar (probably better, TBH) result with something like:
isolde restrain distances #1&(helix|strand)&backbone isolde restrain torsions #1&(helix|strand) sidechain false
The advantage of those is that (a) they’ll work a bit better when the true conformation isn’t *perfect* helix or strand, and (b) they have a lot more flexibility in terms of your ability to fine-tune their behaviour (for models fetched from the Alphafold DB, try adding the argument “adjustForConfidence true” to automatically take the pLDDT and PAE values into account).
— Tristan
On 13 Mar 2022, at 14:42, Guido Hansen via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi all,
I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess:
Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script?
Cheers, Guido
--
PD Dr. Guido Hansen Group Leader [Image removed by sender. Uni-Lübeck]
Universität zu Lübeck Institut für Biochemie
Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen@biochem.uni-luebeck.demailto:hansen@biochem.uni-luebeck.de www.biochem.uni-luebeck.dehttp://www.biochem.uni-luebeck.de
Ratzeburger Allee 160 23562 Lübeck _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users -- PD Dr. Guido Hansen Group Leader [Image removed by sender. Uni-Lübeck]
Universität zu Lübeck Institut für Biochemie
Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen@biochem.uni-luebeck.demailto:hansen@biochem.uni-luebeck.de www.biochem.uni-luebeck.dehttp://www.biochem.uni-luebeck.de
Ratzeburger Allee 160 23562 Lübeck
Hi Matthias,
The “(helix|strand)” selectors are core ChimeraX rather than ISOLDE. Beyond that, the answer is “it depends”. As I understand it, if the model has HELIX or STRAND records (or the mmCIF equivalents) then ChimeraX will respect those when first loading the model. If they don’t exist it will use dssp to calculate them. If dssp is used subsequently it will recalculate the secondary structure based on the current conformation - as far as I know once that’s happened there’s no way to reinstate the original definitions.
Best, Tristan
On Fri, 17 Nov 2023 at 11:19, Vorländer,Matthias Kopano via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I would like to pick up this old thread. Do I interpret this correctly that ISOLDE ignores the secondary structure annotations in the PDB header and has its own way of calculating what’s a helix and a strand? If so, are these definitions written in the PDB header when the file is saved, or is there an option to do so?
Many thanks,
Matthias
*From: *ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Tristan Croll via ChimeraX-users chimerax-users@cgl.ucsf.edu *Date: *Tuesday, 15. March 2022 at 17:30 *To: *Guido Hansen hansen@biochem.uni-luebeck.de *Cc: *chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu *Subject: *Re: [chimerax-users] ISOLDE and secondary structure restraints
Oops! My bad - was responding on the move, and forgetting my own implementation. You're right, the "isolde restrain distances" command works on a per-residue basis, so sidechain atoms will be included regardless. On the other hand, the "isolde release distances" command works per-atom, so after the restrain command you can selectively release the sidechain restraints with:
isolde release distances #1&sideonly
*From:* Guido Hansen hansen@biochem.uni-luebeck.de *Sent:* 15 March 2022 16:20 *To:* Tristan Croll tic20@cam.ac.uk *Cc:* chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu *Subject:* Re: [chimerax-users] ISOLDE and secondary structure restraints
Thanks for your suggestions. However, I think that when applying distance restraints using the command below also distances of mainchain atoms of secondary structure elements to nearby sidechain atoms get restrainted.
isolde restrain distances #1&(helix|strand)&backbone
What you get when using the gui is something like that:
-- Guido
Am 13.03.2022 um 16:07 schrieb Tristan Croll:
Not the hard-coded helix and beta-sheet restraints, I’m afraid. But you can get a very similar (probably better, TBH) result with something like:
isolde restrain distances #1&(helix|strand)&backbone
isolde restrain torsions #1&(helix|strand) sidechain false
The advantage of those is that (a) they’ll work a bit better when the true conformation isn’t *perfect* helix or strand, and (b) they have a lot more flexibility in terms of your ability to fine-tune their behaviour (for models fetched from the Alphafold DB, try adding the argument “adjustForConfidence true” to automatically take the pLDDT and PAE values into account).
— Tristan
On 13 Mar 2022, at 14:42, Guido Hansen via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi all,
I just started model building in cryoEM maps and get great results using ISOLDE on AlphaFold2-derived initial models. I have a question which is mainly directed to Tristan I guess:
Is is possible to use the command line/script to apply secondary structure restraints in ISOLDE? I would like to restrain the initial secondary structure assignment from Alphafold especially at resolution worse than 3.5 A. At the moment I select each and every residue range assigned to helix, parallel or antiparallel beta-strand one after the other and turn on the corresponding restrains in the ISOLDE GUI. Is there a better way via command line of script?
Cheers, Guido
--
*PD Dr. Guido Hansen* Group Leader
[image: Image removed by sender. Uni-Lübeck]
*Universität zu Lübeck* *Institut für Biochemie*
Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen@biochem.uni-luebeck.de www.biochem.uni-luebeck.de
Ratzeburger Allee 160 https://www.google.com/maps/search/Ratzeburger+Allee+160+%0D%0A23562+L%C3%BCbeck?entry=gmail&source=g 23562 Lübeck https://www.google.com/maps/search/Ratzeburger+Allee+160+%0D%0A23562+L%C3%BCbeck?entry=gmail&source=g
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
--
*PD Dr. Guido Hansen*
Group Leader
[image: Image removed by sender. Uni-Lübeck]
*Universität zu Lübeck* *Institut für Biochemie*
Tel +49 451 3101 3122 Fax +49 451 3101 3104 E-Mail hansen@biochem.uni-luebeck.de www.biochem.uni-luebeck.de
Ratzeburger Allee 160 https://www.google.com/maps/search/Ratzeburger+Allee+160+%0D%0A23562+L%C3%BCbeck?entry=gmail&source=g 23562 Lübeck https://www.google.com/maps/search/Ratzeburger+Allee+160+%0D%0A23562+L%C3%BCbeck?entry=gmail&source=g _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
participants (4)
-
Guido Hansen -
Tristan Croll -
Tristan Croll -
Vorländer,Matthias Kopano