Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system

[Xiang-Jun Lu <3d...@gm...>]

> Message: 1
> Date: Thu, 11 Nov 2021 01:21:47 +0000
> From: "Mooers, Blaine H.M.  (HSC)" <Bla...@ou...>
> To: amirhossein taghavi <tag...@gm...>,
>         "pym...@li..."
>         <pym...@li...>
> Subject: Re: [PyMOL] [EXTERNAL]  create a 26 bp RNA from a 13 bp
>         system
> Message-ID:
>         <
> 87D...@CO...>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Amir,
>
> No, not automatically. Your RNA is very distorted from
> the standard A-form. I doubt any modeling program
> can accurately extend such a distorted helix. Maybe
> someone else will prove me wrong.
>
>
DSSR was used to create the attached 26-base-pair (bp) long RNA by
duplicating the initial 13-bp model. I'm not sure whether this is the
outcome Amir was hoping for.

Best regards,

Xiang-Jun

--
Xiang-Jun Lu (Ph.D.)
Email: xia...@x3...
Web: http://x3dna.org/
Forum: http://forum.x3dna.org/

 Your RNA does not have the expected
> doughnut cross-section of the A-form when
> viewed down the helical axis.
>
> Your model has triclinic unit cell dimensions on the first line of the
> coordinate file.
> Is it from a crystal structure? If it is, it might be stacked
> end-on-end in the crystal lattice. You could generate its
> symmetry mate and save its coordinates.
> However, the cryst card in your file is corrupted, and
> PyMOL cannot use it to generate symmetry mates.
>
> You can align the terminal base pairs manually through a
> series of commands. If you try by dragging one copy
> relative to another, you will wind up pulling out all of your
> hair. The commands and patience will keep you out  of the mad house.
>
> load model_.pdb
> orient
> # align along the x-axis
> copy model2, model_
> translate [38,0,0], model2
> rotate x, -45, model2
>
> Issue a series of subsequent translate, rotate, and orient commands as
> needed.
> Use smaller increments like 1 or 2 angstroms and 5 or 10 degrees.
> The angle between the terminal base pairs should be about 33 degrees.
> With patience, you can do this in less than an hour.
>
> However, I am not sure how relevant the duplicated structure will be given
> the distortions in model_.pdb.
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology, College of Medicine
> Director of the Laboratory of Biomolecular Structure and Function
> Academic Director, Biomolecular Structure Core, COBRE in Structural Biology
> Full Member, Cancer Biology Program, Stephenson Cancer Center
> University of Oklahoma Health Sciences Center
>
> Mailing Address:
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> Oklahoma City, OK 73104-5419
> Office: 405-271-8300 Lab: 405-271-8312
>
> Websites:
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> COBRE in Structural Biology: https://www.ou.edu/structuralbiology
> ________________________________________
> From: amirhossein taghavi [tag...@gm...]
> Sent: Wednesday, November 10, 2021 5:03 PM
> To: pym...@li...
> Subject: [EXTERNAL] [PyMOL] create a 26 bp RNA from a 13 bp system
>
> Hello,
>
> I have an RNA duplex with 13 base-pairs (attached). Is it possible to
> duplicate this system and then fuse the two molecules to create a 26
> base-pair long system using the pymol.
>
> Thanks in advance.
>
> Cheers,
> Amir
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 10 Nov 2021 21:44:21 -0500
> From: amirhossein taghavi <tag...@gm...>
> To: "Mooers, Blaine H.M. (HSC)" <Bla...@ou...>
> Cc: "pym...@li..."
>         <pym...@li...>
> Subject: Re: [PyMOL] [EXTERNAL]  create a 26 bp RNA from a 13 bp
>         system
> Message-ID:
>         <CAP4-oUjYJ-PbCdeoBsOJ3=cnEje_7vwhTWGVitxd=
> gK6...@ma...>
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>
> Hello Prof. Blaine,
>
> Thanks a lot for the detailed explanation. The model is out of MD
> simulations with the box information.
> I will try the workflow you suggested.
> I very much appreciate your help.
>
> Best regards,
> Amir
>
>
>