[Chimera-users] Joining fragments in a peptide bond

Sujata sujata.sovani at gmail.com
Tue Sep 21 10:22:18 PDT 2010

Thank you very much Elaine for your detailed reply.


On Mon, Sep 20, 2010 at 4:06 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Sujata,
> I'll answer the easy part first: you can specify the axis cylinder radius
> as an Angstrom value in the Define Axis dialog (opened from the
> Axes/Planes/Centroids tool) or if you are using the "define" command, with
> the "radius" keyword, see the general options in that page:
> <
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes
> >
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/define.html>
> I see you have a left-handed polyproline helix which also has a
> superhelical twist, and you wish to extend its length maintaining the same
> helicity and superhelicity.  Then you have assembled three of these into a
> triple helix.  This problem is not really something you want to attack with
> Build Structure; instead, you need to figure out the symmetry operations to
> extend this structure, then apply them to additional copies of the identical
> structure to extend it.
> One way would be to figure out BIOMT matrices and add those to the PDB
> file.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html#biomt>
> However, it can be difficult to figure out the correct values and edit them
> in using the correct format, so I'll describe a different way that just uses
> commands.
> The two fragments you sent are identical (I know you know this, I'm just
> explaining to the others), and I matched the first half of one copy to the
> second half of the other copy to try to figure out the symmetry operations.
>  Command:
> match #1:1-15 at ca #0:16-30 at ca
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html>
> This match looked pretty good to me, so next I used the measure command to
> tell me the transformation that had been used to generate this match:
> measure rotation #0 #1
> <
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#rotation
> >
> Actually that command will display another axis cylinder, and I don't think
> you can control the size of that one, but you can just close or hide it with
> the Model Panel (under Favorites in the menu).  The transformation
> information is given in the Reply Log (also under Favorites in the menu):
> Position of #1 relative to #0 coordinates:
>  Matrix rotation and translation
>    -0.00777505  -0.89851915  -0.43886545  45.94850252
>     0.89297961  -0.20375330   0.40133777  -0.02182236
>    -0.45002996  -0.38877748   0.80394347 -26.28870812
>  Axis  -0.40352597   0.00570191   0.91495042
>  Axis point  17.07887792  12.85324577   0.00000000
>  Rotation angle (degrees) 101.75881858
>  Shift along axis -42.59440324
> Then I reset so that the two fragments were again exactly superimposed
> (since they are identical ), using the command:
> reset
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/reset.html>
> Then I applied TWICE the reported translation and rotation because the
> match was of 15 residues, but the whole fragment is 30 and I want to join
> the ends.  I used the axis given in the Reply Log as the axis of movement
> and the axis point as the center of rotation, and applied twice the rotation
> angle with the "turn" command and twice the shift with the "move" command:
> turn   -0.40352597,0.00570191,0.91495042 203.5 models #1 coord 0 center
> 17.07887792,12.85324577,0
> move  -0.40352597,0.00570191,0.91495042 85.188 models #1 coord 0
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/turn.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/move.html>
> At this point it looks like they are in a pretty good position to just add
> the bond and delete the extra atoms at the ends.   Since you already have
> the models in position, don't use Join Models in Build Structure.  Instead
> use "copy/combine" in the Model Panel (or the "combine" command) to merge
> the two fragments to create another model, and in that model, select the
> extra atoms that you want to delete (probably all hydrogens on N-term N and
> one of the oxygens on the C-term carboxyl of the other fragment), use
> command "del sel" to delete them, then select the two atoms to be bonded,
> and use command "bond sel".  The bond will look a little strained, but this
> whole approach is going to get you an APPROXIMATE model.  You could use
> command "addh" if you cared about the presence of the amide hydrogen at the
> join.   This approximate model is good enough for a figure, or as a starting
> point for a simulation in some other package like Amber.
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html>
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/addh.html>
> Actually, it might have been better to start with the trimeric fragment
> with all 3 chains, use residues from all 3 chains for the match, etc., and
> then there would be three bonds to form, rather than repeating only the
> single strand and then trimerizing.  Hard to know without trying.  Sorry, it
> is a rather laborious process.
> I hope this helps,
> 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 Sep 20, 2010, at 10:31 AM, Sujata wrote:
>  > Hello Elaine,
> > Thank you for the email below. It was very helpful.
> >
> > But, I would like the second fragment to be on the same helical axis as
> the first one. When I join them this way, by defining the torsion angle, the
> second one does not stay on the same axis as the first one. So is there a
> way that I can fix the two peptides to be on the same axis when I fix the
> bond length and the torsion?
> >
> > I am attaching the two individual files and the combined one.
> >
> > Also when one defines axis, is there a way to reduce the thickness of the
> displayed axis. Due to its thickness, the atoms are not visible.
> >  Thank you.
> >
> > Regards,
> > Sujata
> >
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