How do you refine a structure with a new (or modified) amino acid residue in Isolde
Hi Everyone, I am adding residues (essentially modified cysteines ) to the polypeptide chain. e.g. HETATM 1 N2 PGR 0 1.743 -1.624 -0.731 1.00 0.00 N HETATM 2 C1 PGR 0 -0.077 -0.207 -0.018 1.00 0.00 C HETATM 3 C2 PGR 0 1.394 -0.544 0.203 1.00 0.00 C HETATM 4 C3 PGR 0 -0.485 0.927 -0.717 1.00 0.00 C HETATM 5 C4 PGR 0 -1.034 -1.073 0.503 1.00 0.00 C HETATM 6 C5 PGR 0 -1.840 1.189 -0.887 1.00 0.00 C HETATM 7 C6 PGR 0 -2.389 -0.810 0.331 1.00 0.00 C HETATM 8 C7 PGR 0 -2.794 0.323 -0.364 1.00 0.00 C HETATM 9 C8 PGR 0 2.379 0.585 -0.085 1.00 0.00 C HETATM 10 H1 PGR 0 1.529 -0.961 1.213 1.00 0.00 H HETATM 11 H2 PGR 0 0.232 1.599 -1.120 1.00 0.00 H HETATM 12 H3 PGR 0 -0.727 -1.940 1.035 1.00 0.00 H HETATM 13 H4 PGR 0 -2.145 2.053 -1.418 1.00 0.00 H HETATM 14 H5 PGR 0 -3.116 -1.477 0.733 1.00 0.00 H HETATM 15 H6 PGR 0 -3.837 0.527 -0.497 1.00 0.00 H HETATM 16 H7 PGR 0 1.655 -1.298 -1.705 1.00 0.00 H HETATM 17 H8 PGR 0 1.143 -2.449 -0.581 1.00 0.00 H HETATM 18 O18 PGR 0 3.393 0.026 -0.528 1.00 0.00 O HETATM 19 SG PGR 0 2.777 1.511 1.356 1.00 0.00 S HETATM 20 CB PGR 0 1.349 2.524 1.801 1.00 0.00 C HETATM 21 CA PGR 0 1.698 3.446 2.926 1.00 0.00 C HETATM 22 N PGR 0 0.565 4.254 3.182 1.00 0.00 N HETATM 23 C PGR 0 2.646 4.407 2.450 1.00 0.00 C HETATM 24 O24 PGR 0 2.145 5.309 1.717 1.00 0.00 O HETATM 25 O25 PGR 0 3.976 4.409 2.828 1.00 0.00 O HETATM 26 H9 PGR 0 1.980 1.252 -0.806 1.00 0.00 H HETATM 27 H11 PGR 0 1.044 3.140 0.942 1.00 0.00 H HETATM 28 H12 PGR 0 0.527 1.867 2.099 1.00 0.00 H HETATM 29 H13 PGR 0 2.043 2.881 3.803 1.00 0.00 H HETATM 30 H14 PGR 0 -0.245 3.721 3.480 1.00 0.00 H HETATM 31 H15 PGR 0 0.359 4.821 2.336 1.00 0.00 H TER My question is: How do I set up Isolde so that it can refine the structure?
Many thanks, Trevor Sewell
Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/report-incident
Unfortunately, the answer is that right now you don’t - ISOLDE currently only helps you parameterise new organic ligands that *aren’t* covalently bonded to anything else. We’re currently discussing a new, much more general solution, but for now you’d really need to recruit the help of a force field specialist to get that happening. If you *do* know someone who can help you parameterise this residue for AMBER, get back to me and I can talk you through incorporating it into ISOLDE’s force field.
Best, Tristan
On Tue, 25 Jul 2023 at 16:17, Trevor Sewell via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Everyone,
I am adding residues (essentially modified cysteines ) to the polypeptide chain.
e.g.
HETATM 1 N2 PGR 0 1.743 -1.624 -0.731 1.00 0.00 N
HETATM 2 C1 PGR 0 -0.077 -0.207 -0.018 1.00 0.00 C
HETATM 3 C2 PGR 0 1.394 -0.544 0.203 1.00 0.00 C
HETATM 4 C3 PGR 0 -0.485 0.927 -0.717 1.00 0.00 C
HETATM 5 C4 PGR 0 -1.034 -1.073 0.503 1.00 0.00 C
HETATM 6 C5 PGR 0 -1.840 1.189 -0.887 1.00 0.00 C
HETATM 7 C6 PGR 0 -2.389 -0.810 0.331 1.00 0.00 C
HETATM 8 C7 PGR 0 -2.794 0.323 -0.364 1.00 0.00 C
HETATM 9 C8 PGR 0 2.379 0.585 -0.085 1.00 0.00 C
HETATM 10 H1 PGR 0 1.529 -0.961 1.213 1.00 0.00 H
HETATM 11 H2 PGR 0 0.232 1.599 -1.120 1.00 0.00 H
HETATM 12 H3 PGR 0 -0.727 -1.940 1.035 1.00 0.00 H
HETATM 13 H4 PGR 0 -2.145 2.053 -1.418 1.00 0.00 H
HETATM 14 H5 PGR 0 -3.116 -1.477 0.733 1.00 0.00 H
HETATM 15 H6 PGR 0 -3.837 0.527 -0.497 1.00 0.00 H
HETATM 16 H7 PGR 0 1.655 -1.298 -1.705 1.00 0.00 H
HETATM 17 H8 PGR 0 1.143 -2.449 -0.581 1.00 0.00 H
HETATM 18 O18 PGR 0 3.393 0.026 -0.528 1.00 0.00 O
HETATM 19 SG PGR 0 2.777 1.511 1.356 1.00 0.00 S
HETATM 20 CB PGR 0 1.349 2.524 1.801 1.00 0.00 C
HETATM 21 CA PGR 0 1.698 3.446 2.926 1.00 0.00 C
HETATM 22 N PGR 0 0.565 4.254 3.182 1.00 0.00 N
HETATM 23 C PGR 0 2.646 4.407 2.450 1.00 0.00 C
HETATM 24 O24 PGR 0 2.145 5.309 1.717 1.00 0.00 O
HETATM 25 O25 PGR 0 3.976 4.409 2.828 1.00 0.00 O
HETATM 26 H9 PGR 0 1.980 1.252 -0.806 1.00 0.00 H
HETATM 27 H11 PGR 0 1.044 3.140 0.942 1.00 0.00 H
HETATM 28 H12 PGR 0 0.527 1.867 2.099 1.00 0.00 H
HETATM 29 H13 PGR 0 2.043 2.881 3.803 1.00 0.00 H
HETATM 30 H14 PGR 0 -0.245 3.721 3.480 1.00 0.00 H
HETATM 31 H15 PGR 0 0.359 4.821 2.336 1.00 0.00 H
TER
My question is: How do I set up Isolde so that it can refine the structure?
Many thanks,
Trevor Sewell
Disclaimer - University of Cape Town This email is subject to UCT policies and email disclaimer published on our website at http://www.uct.ac.za/main/email-disclaimer or obtainable from +27 21 650 9111. If this email is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via https://csirt.uct.ac.za/report-incident _______________________________________________ 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 (2)
-
Trevor Sewell -
Tristan Croll