[Dock-fans] [Dockdev] How to select Spheres around a specific AA residue.

RKH Liyanage rkhliyanage at gmail.com
Sun Apr 23 21:29:33 PDT 2017


*Thank you very much again!*
I was able to select the spheres around the loop of AA residues.

Regards!



On 24 April 2017 at 08:43, Trent E. Balius <tbalius at aol.com> wrote:

> One way to do this is to isolate your residue of interest and save it as a
> mol2 file.
>
> To do this open up your protein in chimera.
>   open 1A2B
>
> Delete every thing but the residue of interest (here residue 118 in chain
> A).
>   sel #0:.A & :118
>   del ~sel
>
> Write the residue out as a mol2 file:
>   write format mol2 #0 1A2B.118.mol2
>
> Open the residue back up to make sure that the frame has not shifted (do
> not move the frame of the protein during the above commands).
>
> Then use this mol2 file when selecting the spheres:
>     sphere_selector 1A2B.rec.sph 1A2B.118.mol2 8.0
>
> I hope that this helps,
>
> Trent
>
> ======================================
> Trent E. Balius, PhD
> Postdoc, Shoichet Lab,
> Dept. Pharm. Chem., UCSF
> Phone: (415) 514-4253
> URL: http://docking.org/~tbalius
> ======================================
>
>
> -----Original Message-----
> From: RKH Liyanage <rkhliyanage at gmail.com>
> To: dock-fans <dock-fans at docking.org>; dockdev <
> dockdev at mailman.docking.org>
> Sent: Sun, Apr 23, 2017 12:19 pm
> Subject: [Dockdev] How to select Spheres around a specific AA residue.
>
> Hi
>
> I want to select spheres around specific amino acid residue manually.
> What should I do to achieve this.
>
> I'm following the tutorial given below.
>
> http://ringo.ams.sunysb.edu/index.php/2015_DOCK_tutorial_
> with_Poly(ADP-ribose)_polymerase_(PARP)
> http://ringo.ams.sunysb.edu/index.php/2017_DOCK_tutorial_
> 1_with_PDB_4QMZ_NEW
>
> Sphere selector selects the spheres automatically.
> How do i change this to select Spheres around a specific Amino Acid
> residue.
> Eg: around AA residue 215 and that loop.
>
> Thanks in advance.
>
> Regards!
> _______________________________________________
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> Dockdev at mailman.docking.org
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>
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