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 On Wed, Nov 10, 2021 at 8:21 PM Mooers, Blaine H.M. (HSC) < blaine-moo...@ouhsc.edu> wrote: > 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. > > 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: > 975 NE 10th Street, BRC 466 > Oklahoma City, OK 73104-5419 > Office: 405-271-8300 Lab: 405-271-8312 > > Websites: > Faculty page: > https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd > BSC-OKC > <https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phdBSC-OKC> > (LBSF): > https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function > COBRE in Structural Biology: https://www.ou.edu/structuralbiology > ________________________________________ > From: amirhossein taghavi [taghavi.amirhoss...@gmail.com] > Sent: Wednesday, November 10, 2021 5:03 PM > To: pymol-users@lists.sourceforge.net > 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 >
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