[Chimera-users] building and positioning disordered sequence

[thereal 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 at n,ca,c,o #0:627.C at n,ca,c,o
match #1.2:216 at n,ca,c,o #0:455.C at 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 at C#2:182.B at 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 at n,ca,c,o #0:648.F at n,ca,c,o

thanks for your help




On Wed, May 4, 2016 at 10:08 AM, thereal sisterdot <
therealsisterdot at 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 at 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/modeller.html#building
>> >
>>
>> 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.html
>> >
>> <
>> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start
>> >
>> <
>> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#adjust
>> >
>> <
>> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movemode/movemode.html
>> >
>> <
>> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html
>> >
>>
>> 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 at 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
>>
>>
>
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