Hi Xiang-Jun Lu, Thanks for proving me wrong. Congratulations on your duplicated model! Please share the commands that you used with DSSR to generate the duplicated helix.
PyMOL does not generate the cartoon representation for the backbones of your duplicate helix. Do you know why? 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 (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function COBRE in Structural Biology: https://www.ou.edu/structuralbiology ________________________________________ From: Xiang-Jun Lu [3dna...@gmail.com] Sent: Friday, November 12, 2021 8:05 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system Message: 1 Date: Thu, 11 Nov 2021 01:21:47 +0000 From: "Mooers, Blaine H.M. (HSC)" <blaine-moo...@ouhsc.edu<mailto:blaine-moo...@ouhsc.edu>> To: amirhossein taghavi <taghavi.amirhoss...@gmail.com<mailto:taghavi.amirhoss...@gmail.com>>, "pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>" <pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>> Subject: Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system Message-ID: <87dcc6c40b22804192b6892e6429ec5f019d5e3...@countach.hsc.net.ou.edu<mailto:87dcc6c40b22804192b6892e6429ec5f019d5e3...@countach.hsc.net.ou.edu>> 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: xiang...@x3dna.org<mailto:xiang...@x3dna.org> Web: http://x3dna.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__x3dna.org_&d=DwMFaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=SezBp4UL1C-pr1f35s70RAkgFpWQaaVnI3ISWKOA7wkFTZWpjoYN2QWKHvmvgwa4&s=SCbMW3JwZkTKAxEfPB8w5TtSItCw4MMTIOr8sxCVEIE&e=> Forum: http://forum.x3dna.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__forum.x3dna.org_&d=DwMFaQ&c=qKdtBuuu6dQK9MsRUVJ2DPXW6oayO8fu4TfEHS8sGNk&r=rxarJ7aLyHGI62pje1gd6hPxYn9Xv-2lWNWh_1Owonw&m=SezBp4UL1C-pr1f35s70RAkgFpWQaaVnI3ISWKOA7wkFTZWpjoYN2QWKHvmvgwa4&s=R5l09hlMu8Qv8Uw7eKpaBtB-k1s-E1xX0jqFJ9b_oDg&e=> 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<mailto:taghavi.amirhoss...@gmail.com>] Sent: Wednesday, November 10, 2021 5:03 PM To: pymol-users@lists.sourceforge.net<mailto: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 ------------------------------ Message: 2 Date: Wed, 10 Nov 2021 21:44:21 -0500 From: amirhossein taghavi <taghavi.amirhoss...@gmail.com<mailto:taghavi.amirhoss...@gmail.com>> To: "Mooers, Blaine H.M. (HSC)" <blaine-moo...@ouhsc.edu<mailto:blaine-moo...@ouhsc.edu>> Cc: "pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>" <pymol-users@lists.sourceforge.net<mailto:pymol-users@lists.sourceforge.net>> Subject: Re: [PyMOL] [EXTERNAL] create a 26 bp RNA from a 13 bp system Message-ID: <CAP4-oUjYJ-PbCdeoBsOJ3=cnEje_7vwhTWGVitxd=gk6d9b...@mail.gmail.com<mailto:gk6d9b...@mail.gmail.com>> Content-Type: text/plain; charset="utf-8" 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 _______________________________________________ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
