Export Isolde residue paramters (xml) for phenix
Hello, Sorry If this has been asked recently and I missed it, but is there a way to convert the residues parameter XML file created by Isolde (for a ligand) into a restraints file that can be used in the phenix realspace refinement? Sean
I'm afraid not. MD parameters are more difficult to transfer to the traditional crystallographic restraint schemes than you might first think. You'll need to use one of the dedicated restraint generation tools like phenix.elbow or CCP4's AceDRG. Using eLBOW, for more complicated ligands I've generally gotten best results in the past by using its optional plugin to ORCA (https://www.faccts.de/docs/orca/5.0/tutorials/). -- Tritan On Tue, Oct 17, 2023 at 11:04 AM Sean Connell via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
Sorry If this has been asked recently and I missed it, but is there a way to convert the residues parameter XML file created by Isolde (for a ligand) into a restraints file that can be used in the phenix realspace refinement?
Sean _______________________________________________ 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/
-- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
Thanks for the tip! and the quick response :) On Tue, 17 Oct 2023 at 12:20, Tristan Croll <tcroll@altoslabs.com> wrote:
I'm afraid not. MD parameters are more difficult to transfer to the traditional crystallographic restraint schemes than you might first think. You'll need to use one of the dedicated restraint generation tools like phenix.elbow or CCP4's AceDRG. Using eLBOW, for more complicated ligands I've generally gotten best results in the past by using its optional plugin to ORCA (https://www.faccts.de/docs/orca/5.0/tutorials/).
-- Tritan
On Tue, Oct 17, 2023 at 11:04 AM Sean Connell via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
Sorry If this has been asked recently and I missed it, but is there a way to convert the residues parameter XML file created by Isolde (for a ligand) into a restraints file that can be used in the phenix realspace refinement?
Sean _______________________________________________ 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/
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
Good Morning. I have two more quick questions about using Isolde: 1) Can another model be used as a template for the 'isolde restrain basepairs' command? 2) is there a way to set restraints to coordinate the waters around a Mg ion, for example (i.e. so they have the correct geometry)? On Tue, 17 Oct 2023 at 12:20, Tristan Croll <tcroll@altoslabs.com> wrote:
I'm afraid not. MD parameters are more difficult to transfer to the traditional crystallographic restraint schemes than you might first think. You'll need to use one of the dedicated restraint generation tools like phenix.elbow or CCP4's AceDRG. Using eLBOW, for more complicated ligands I've generally gotten best results in the past by using its optional plugin to ORCA (https://www.faccts.de/docs/orca/5.0/tutorials/).
-- Tritan
On Tue, Oct 17, 2023 at 11:04 AM Sean Connell via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
Sorry If this has been asked recently and I missed it, but is there a way to convert the residues parameter XML file created by Isolde (for a ligand) into a restraints file that can be used in the phenix realspace refinement?
Sean _______________________________________________ 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/
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
1) No - but the “isolde restrain distances” command also works on nucleic acids, and does accept templates. Should give you essentially the same effect, plus some extra reinforcement of local geometry. 2) Not really - and I’m aware this is a deficiency. In general metal ions don’t behave all that well in classical MD - the parameterisation simply isn’t rich enough to capture their intricacies. I’d love to find a better solution (and to find the time to implement it), but right now the best that’s really possible is to manually add distance restraints between the metal and surrounding atoms. You can add and adjust these using the “simple distance restraints” widget. For these I’d suggest increasing the spring constant quite a bit (try 250 or 500). — Tristan On Sat, 21 Oct 2023 at 08:02, Sean Connell <sean.connell@gmail.com> wrote:
Good Morning. I have two more quick questions about using Isolde:
1) Can another model be used as a template for the 'isolde restrain basepairs' command?
2) is there a way to set restraints to coordinate the waters around a Mg ion, for example (i.e. so they have the correct geometry)?
On Tue, 17 Oct 2023 at 12:20, Tristan Croll <tcroll@altoslabs.com> wrote:
I'm afraid not. MD parameters are more difficult to transfer to the traditional crystallographic restraint schemes than you might first think. You'll need to use one of the dedicated restraint generation tools like phenix.elbow or CCP4's AceDRG. Using eLBOW, for more complicated ligands I've generally gotten best results in the past by using its optional plugin to ORCA (https://www.faccts.de/docs/orca/5.0/tutorials/).
-- Tritan
On Tue, Oct 17, 2023 at 11:04 AM Sean Connell via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
Sorry If this has been asked recently and I missed it, but is there a way to convert the residues parameter XML file created by Isolde (for a ligand) into a restraints file that can be used in the phenix realspace refinement?
Sean _______________________________________________ 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/
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT <https://www.google.com/maps/search/1+Ashley+Road,+Altrincham,+Cheshire,+Unit...>
-- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
Thank you, that is very helpful. Regarding the the metal constraints, to set up the distance constraints is a good plan to parse the output from Phenix.metal_coordination? Is the a command for the simple distance restraints 'isolde_restrain_single_distance' or is there something better for a simple distance? On Sat, 21 Oct 2023 at 09:28, Tristan Croll <tcroll@altoslabs.com> wrote:
1) No - but the “isolde restrain distances” command also works on nucleic acids, and does accept templates. Should give you essentially the same effect, plus some extra reinforcement of local geometry.
2) Not really - and I’m aware this is a deficiency. In general metal ions don’t behave all that well in classical MD - the parameterisation simply isn’t rich enough to capture their intricacies. I’d love to find a better solution (and to find the time to implement it), but right now the best that’s really possible is to manually add distance restraints between the metal and surrounding atoms. You can add and adjust these using the “simple distance restraints” widget. For these I’d suggest increasing the spring constant quite a bit (try 250 or 500).
— Tristan
On Sat, 21 Oct 2023 at 08:02, Sean Connell <sean.connell@gmail.com> wrote:
Good Morning. I have two more quick questions about using Isolde:
1) Can another model be used as a template for the 'isolde restrain basepairs' command?
2) is there a way to set restraints to coordinate the waters around a Mg ion, for example (i.e. so they have the correct geometry)?
On Tue, 17 Oct 2023 at 12:20, Tristan Croll <tcroll@altoslabs.com> wrote:
I'm afraid not. MD parameters are more difficult to transfer to the traditional crystallographic restraint schemes than you might first think. You'll need to use one of the dedicated restraint generation tools like phenix.elbow or CCP4's AceDRG. Using eLBOW, for more complicated ligands I've generally gotten best results in the past by using its optional plugin to ORCA (https://www.faccts.de/docs/orca/5.0/tutorials/).
-- Tritan
On Tue, Oct 17, 2023 at 11:04 AM Sean Connell via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
Sorry If this has been asked recently and I missed it, but is there a way to convert the residues parameter XML file created by Isolde (for a ligand) into a restraints file that can be used in the phenix realspace refinement?
Sean _______________________________________________ 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/
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT <https://www.google.com/maps/search/1+Ashley+Road,+Altrincham,+Cheshire,+Unit...>
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
No, I'm afraid there's no command for the simple distance restraints at present - those are GUI-only. There's nothing stopping you using the "isolde restrain single distance" command, of course - in fact, that might even be preferable since you could then give your metal restraints their own group name. If you set the "confidence" parameter to 2 and make *minDist* equal to *maxDist* then the restraint will behave identically to a standard harmonic distance restraint. So your command for a single atom pair would look something like: isolde restrain single dist {atomspec} 2.1 2.1 confidence 2 wellHalfWidth 0.1 strength 200 groupName "Metal Restraints" Setting the group name is optional, but will prevent you accidentally releasing your metal restraints alongside any reference restraints you might be using. In the "Manage/Release Adaptive Restraints" widget on the GUI you'll also be able to give them their own colour scheme. On Sat, Oct 21, 2023 at 9:17 AM Sean Connell <sean.connell@gmail.com> wrote:
Thank you, that is very helpful.
Regarding the the metal constraints, to set up the distance constraints is a good plan to parse the output from Phenix.metal_coordination? Is the a command for the simple distance restraints 'isolde_restrain_single_distance' or is there something better for a simple distance?
On Sat, 21 Oct 2023 at 09:28, Tristan Croll <tcroll@altoslabs.com> wrote:
1) No - but the “isolde restrain distances” command also works on nucleic acids, and does accept templates. Should give you essentially the same effect, plus some extra reinforcement of local geometry.
2) Not really - and I’m aware this is a deficiency. In general metal ions don’t behave all that well in classical MD - the parameterisation simply isn’t rich enough to capture their intricacies. I’d love to find a better solution (and to find the time to implement it), but right now the best that’s really possible is to manually add distance restraints between the metal and surrounding atoms. You can add and adjust these using the “simple distance restraints” widget. For these I’d suggest increasing the spring constant quite a bit (try 250 or 500).
— Tristan
On Sat, 21 Oct 2023 at 08:02, Sean Connell <sean.connell@gmail.com> wrote:
Good Morning. I have two more quick questions about using Isolde:
1) Can another model be used as a template for the 'isolde restrain basepairs' command?
2) is there a way to set restraints to coordinate the waters around a Mg ion, for example (i.e. so they have the correct geometry)?
On Tue, 17 Oct 2023 at 12:20, Tristan Croll <tcroll@altoslabs.com> wrote:
I'm afraid not. MD parameters are more difficult to transfer to the traditional crystallographic restraint schemes than you might first think. You'll need to use one of the dedicated restraint generation tools like phenix.elbow or CCP4's AceDRG. Using eLBOW, for more complicated ligands I've generally gotten best results in the past by using its optional plugin to ORCA (https://www.faccts.de/docs/orca/5.0/tutorials/).
-- Tritan
On Tue, Oct 17, 2023 at 11:04 AM Sean Connell via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
Sorry If this has been asked recently and I missed it, but is there a way to convert the residues parameter XML file created by Isolde (for a ligand) into a restraints file that can be used in the phenix realspace refinement?
Sean _______________________________________________ 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/
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT <https://www.google.com/maps/search/1+Ashley+Road,+Altrincham,+Cheshire,+Unit...>
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
-- Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
Thank you for the explanation. I really appreciate the information. sean On Sat, 21 Oct 2023 at 10:32, Tristan Croll <tcroll@altoslabs.com> wrote:
No, I'm afraid there's no command for the simple distance restraints at present - those are GUI-only. There's nothing stopping you using the "isolde restrain single distance" command, of course - in fact, that might even be preferable since you could then give your metal restraints their own group name. If you set the "confidence" parameter to 2 and make *minDist* equal to *maxDist* then the restraint will behave identically to a standard harmonic distance restraint. So your command for a single atom pair would look something like:
isolde restrain single dist {atomspec} 2.1 2.1 confidence 2 wellHalfWidth 0.1 strength 200 groupName "Metal Restraints"
Setting the group name is optional, but will prevent you accidentally releasing your metal restraints alongside any reference restraints you might be using. In the "Manage/Release Adaptive Restraints" widget on the GUI you'll also be able to give them their own colour scheme.
On Sat, Oct 21, 2023 at 9:17 AM Sean Connell <sean.connell@gmail.com> wrote:
Thank you, that is very helpful.
Regarding the the metal constraints, to set up the distance constraints is a good plan to parse the output from Phenix.metal_coordination? Is the a command for the simple distance restraints 'isolde_restrain_single_distance' or is there something better for a simple distance?
On Sat, 21 Oct 2023 at 09:28, Tristan Croll <tcroll@altoslabs.com> wrote:
1) No - but the “isolde restrain distances” command also works on nucleic acids, and does accept templates. Should give you essentially the same effect, plus some extra reinforcement of local geometry.
2) Not really - and I’m aware this is a deficiency. In general metal ions don’t behave all that well in classical MD - the parameterisation simply isn’t rich enough to capture their intricacies. I’d love to find a better solution (and to find the time to implement it), but right now the best that’s really possible is to manually add distance restraints between the metal and surrounding atoms. You can add and adjust these using the “simple distance restraints” widget. For these I’d suggest increasing the spring constant quite a bit (try 250 or 500).
— Tristan
On Sat, 21 Oct 2023 at 08:02, Sean Connell <sean.connell@gmail.com> wrote:
Good Morning. I have two more quick questions about using Isolde:
1) Can another model be used as a template for the 'isolde restrain basepairs' command?
2) is there a way to set restraints to coordinate the waters around a Mg ion, for example (i.e. so they have the correct geometry)?
On Tue, 17 Oct 2023 at 12:20, Tristan Croll <tcroll@altoslabs.com> wrote:
I'm afraid not. MD parameters are more difficult to transfer to the traditional crystallographic restraint schemes than you might first think. You'll need to use one of the dedicated restraint generation tools like phenix.elbow or CCP4's AceDRG. Using eLBOW, for more complicated ligands I've generally gotten best results in the past by using its optional plugin to ORCA (https://www.faccts.de/docs/orca/5.0/tutorials/).
-- Tritan
On Tue, Oct 17, 2023 at 11:04 AM Sean Connell via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello,
Sorry If this has been asked recently and I missed it, but is there a way to convert the residues parameter XML file created by Isolde (for a ligand) into a restraints file that can be used in the phenix realspace refinement?
Sean _______________________________________________ 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/
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT <https://www.google.com/maps/search/1+Ashley+Road,+Altrincham,+Cheshire,+Unit...>
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
Altos Labs UK Limited | England | Company reg 13484917 Registered address: 3rd Floor 1 Ashley Road, Altrincham, Cheshire, United Kingdom, WA14 2DT
participants (2)
-
Sean Connell -
Tristan Croll