Dear Chimera Users, i would like to do something in chimera, that is not exactly science but more graphics :-) i have a known structure with 5 positions that i know are crosslinking to a 100aa intrinsically disordered partner sequence. now just in order to better imagine how the disordered binding partner wraps around the structure, i would like to put 5 lysines in the open space near the known crosslinking positions in the pdb structure, and than somehow build the rest of the disordered partner sequence connecting those lysines. its not about getting a estimate of the structural arrangement of the partner. its just so i can better imagine how the partner sequence extends around the interacting residues (as the residues are not in a patch but really all over the 100 aa) or if the arrangement would be sterically possible. any ideas if and how i could achieve that in chimera ? i know that is sound more like a task for illustrator, but :-) THANKS A LOT!!! sisterdot
Dear sisterdot, Hmmm, this would probably be extremely difficult in Chimera. There isn’t really a way to place residues and then say “build linkers to connect these residues in their current positions.” Although we do have an interface to “missing segment” peptide building with Modeller, that is typically for missing loops when you already have coordinates for most of a structure. The problem is that to use that feature, you would need: (1) the sequence of the whole thing including the lysines open in Multalign Viewer (2) the existing coordinates correctly associated with that sequence, which is practically automatic when you already have most of the protein, but I don’t think it is even possible for individual free-floating residues … and even if you had both of those, if I remember correctly, the building would not automatically avoid the other chain (the PDB structure) and might severely overlap with it. Here’s the docs about building missing loops. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo...> Yet another approach would just be to build a long strand or a long helix in the sequence of your unstructured protein, and then manually drag all or parts of it, and manually rotate backbone torsional angles, to try to get the lysines in the correct vicinities. However, this would probably drive you crazy in rather short order. For building the peptide de novo, see Build Structure (Start Structure section), for moving the whole thing or parts of it, see Movement Mouse Moude, and for rotating torsions, see Adjust Torsions. Then you could try to fix up any severe distortions with Minimize Structure. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht...> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht...> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht...> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movemode/movemode....> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize....> Sorry to be discouraging, just didn’t want to send you on a wild goose chase! But maybe others have some simpler ideas, or can suggest some other program(s) better suited to the task… Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 3, 2016, at 1:31 AM, thereal sisterdot <therealsisterdot@gmail.com> wrote:
Dear Chimera Users,
i would like to do something in chimera, that is not exactly science but more graphics :-)
i have a known structure with 5 positions that i know are crosslinking to a 100aa intrinsically disordered partner sequence.
now just in order to better imagine how the disordered binding partner wraps around the structure, i would like to put 5 lysines in the open space near the known crosslinking positions in the pdb structure, and than somehow build the rest of the disordered partner sequence connecting those lysines.
its not about getting a estimate of the structural arrangement of the partner. its just so i can better imagine how the partner sequence extends around the interacting residues (as the residues are not in a patch but really all over the 100 aa) or if the arrangement would be sterically possible.
any ideas if and how i could achieve that in chimera ? i know that is sound more like a task for illustrator, but :-)
THANKS A LOT!!! sisterdot
Thanks a lot Elaine! If i should find a solution i will make sure to post it! all the best! On Tue, May 3, 2016 at 8:40 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear sisterdot, Hmmm, this would probably be extremely difficult in Chimera. There isn’t really a way to place residues and then say “build linkers to connect these residues in their current positions.” Although we do have an interface to “missing segment” peptide building with Modeller, that is typically for missing loops when you already have coordinates for most of a structure. The problem is that to use that feature, you would need:
(1) the sequence of the whole thing including the lysines open in Multalign Viewer (2) the existing coordinates correctly associated with that sequence, which is practically automatic when you already have most of the protein, but I don’t think it is even possible for individual free-floating residues
… and even if you had both of those, if I remember correctly, the building would not automatically avoid the other chain (the PDB structure) and might severely overlap with it. Here’s the docs about building missing loops. < http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo...
Yet another approach would just be to build a long strand or a long helix in the sequence of your unstructured protein, and then manually drag all or parts of it, and manually rotate backbone torsional angles, to try to get the lysines in the correct vicinities. However, this would probably drive you crazy in rather short order. For building the peptide de novo, see Build Structure (Start Structure section), for moving the whole thing or parts of it, see Movement Mouse Moude, and for rotating torsions, see Adjust Torsions. Then you could try to fix up any severe distortions with Minimize Structure.
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht...
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht...
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht...
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movemode/movemode....
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize....
Sorry to be discouraging, just didn’t want to send you on a wild goose chase! But maybe others have some simpler ideas, or can suggest some other program(s) better suited to the task… Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 3, 2016, at 1:31 AM, thereal sisterdot < therealsisterdot@gmail.com> wrote:
Dear Chimera Users,
i would like to do something in chimera, that is not exactly science but more graphics :-)
i have a known structure with 5 positions that i know are crosslinking to a 100aa intrinsically disordered partner sequence.
now just in order to better imagine how the disordered binding partner wraps around the structure, i would like to put 5 lysines in the open space near the known crosslinking positions in the pdb structure, and than somehow build the rest of the disordered partner sequence connecting those lysines.
its not about getting a estimate of the structural arrangement of the partner. its just so i can better imagine how the partner sequence extends around the interacting residues (as the residues are not in a patch but really all over the 100 aa) or if the arrangement would be sterically possible.
any ideas if and how i could achieve that in chimera ? i know that is sound more like a task for illustrator, but :-)
THANKS A LOT!!! sisterdot
Dear Elaine, this is how i ended up getting approximately what i wanted: #chopped molecule 1 between the lysines (181-182) to be aligned split #1 atoms :126-181 atoms :182-225 #aligned the crosslinks lysines (147,216) with their suggested interaction partners match #1.1:147@n,ca,c,o #0:627.C@n,ca,c,o match #1.2:216@n,ca,c,o #0:455.C@n,ca,c,o combine #1.1-6 name partner # make a long bond between the previously split chain (181-182) sel #2:181.A@C#2:182.B@N bond sel changechains B A #2 write format pdb #2 Partner_Kanchorsconnected.pdb use modeller from the command line to fix the long bond by modelling the loop between the two lysines (148-215) using using https://salilab.org/modeller/manual/node36.html and self.residue_range('148:A', '215:A'), import the modeller result and align it again and match #1:103@n,ca,c,o #0:648.F@n,ca,c,o thanks for your help On Wed, May 4, 2016 at 10:08 AM, thereal sisterdot < therealsisterdot@gmail.com> wrote:
Thanks a lot Elaine!
If i should find a solution i will make sure to post it!
all the best!
On Tue, May 3, 2016 at 8:40 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear sisterdot, Hmmm, this would probably be extremely difficult in Chimera. There isn’t really a way to place residues and then say “build linkers to connect these residues in their current positions.” Although we do have an interface to “missing segment” peptide building with Modeller, that is typically for missing loops when you already have coordinates for most of a structure. The problem is that to use that feature, you would need:
(1) the sequence of the whole thing including the lysines open in Multalign Viewer (2) the existing coordinates correctly associated with that sequence, which is practically automatic when you already have most of the protein, but I don’t think it is even possible for individual free-floating residues
… and even if you had both of those, if I remember correctly, the building would not automatically avoid the other chain (the PDB structure) and might severely overlap with it. Here’s the docs about building missing loops. < http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/mo...
Yet another approach would just be to build a long strand or a long helix in the sequence of your unstructured protein, and then manually drag all or parts of it, and manually rotate backbone torsional angles, to try to get the lysines in the correct vicinities. However, this would probably drive you crazy in rather short order. For building the peptide de novo, see Build Structure (Start Structure section), for moving the whole thing or parts of it, see Movement Mouse Moude, and for rotating torsions, see Adjust Torsions. Then you could try to fix up any severe distortions with Minimize Structure.
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht...
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht...
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.ht...
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movemode/movemode....
< http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize....
Sorry to be discouraging, just didn’t want to send you on a wild goose chase! But maybe others have some simpler ideas, or can suggest some other program(s) better suited to the task… Best, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On May 3, 2016, at 1:31 AM, thereal sisterdot < therealsisterdot@gmail.com> wrote:
Dear Chimera Users,
i would like to do something in chimera, that is not exactly science but more graphics :-)
i have a known structure with 5 positions that i know are crosslinking to a 100aa intrinsically disordered partner sequence.
now just in order to better imagine how the disordered binding partner wraps around the structure, i would like to put 5 lysines in the open space near the known crosslinking positions in the pdb structure, and than somehow build the rest of the disordered partner sequence connecting those lysines.
its not about getting a estimate of the structural arrangement of the partner. its just so i can better imagine how the partner sequence extends around the interacting residues (as the residues are not in a patch but really all over the 100 aa) or if the arrangement would be sterically possible.
any ideas if and how i could achieve that in chimera ? i know that is sound more like a task for illustrator, but :-)
THANKS A LOT!!! sisterdot
participants (2)
-
Elaine Meng -
thereal sisterdot