Hi Patricia, You can add unique segment identifiers to each actin. https://www.biostars.org/p/129381/
You can add these segids by using column selection in a text editor like Visual Studio Code, which is free. Install the BioSyntax plugin to get syntax highlighting of the pdb file. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: patri...@lookfar.ca [patri...@lookfar.ca] Sent: Wednesday, June 03, 2020 12:45 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] [EXTERNAL] Changing Chain ID Thank you Dr. Mooers, That worked! I’ve been trying to solve that for months. I’ve been able to get my protein, linker and actin to fuse. I have now built a chain of five actin and I’m encountering another barrier. I’m attempting to link a protein to each actin, but the program recognizes all 5 linkers as the same linker (all linkers have the same sequence). I’m trying to figure out how to give each linker its own separate name. I’ve searched the mailing group archive and looked at the Alter page you linked for the first solution, but can’t figure out what to do. If you have any further advice that would be much appreciated! Patricia On Tue, 2 Jun 2020 17:49:05 +0000, "Mooers, Blaine H.M. (HSC)" <blaine-moo...@ouhsc.edu> wrote: Hi Patricia, You can copy and paste these commands below one at a time at the upper PyMOL> prompt just below the command history window. Hit return after each paste operation. alter (chain A),chain='F' sort For more information, see https://urldefense.proofpoint.com/v2/url?u=https-3A__pymolwiki.org_index.php-3Ftitle-3DAlter-26redirect-3Dno&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=J3kxkoyQ22CsHFbJcbFrSLohew1yxUPoqMUzfIEHcJU&s=aCIVpCaJYi7T-Ulchmsmp-zOn4dqPHLlwh4sCs8RAAA&e= Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology College of Medicine University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center (BRC) Rm. 466 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 ________________________________________ From: patri...@lookfar.ca [patri...@lookfar.ca] Sent: Tuesday, June 02, 2020 11:49 AM To: pymol-users@lists.sourceforge.net Subject: [EXTERNAL] [PyMOL] Changing Chain ID Hi – I’m a high school student learning to use Pymol for my science fair research, and I’ve been using Pymol for about 6 months. I have been working on attempting to bind a protein to actin for over a month now – but whenever I fuse the linker to the antifreeze protein, it glitches. As well, when I save my actin chain with all the linkers fused as a PDB file and reopen it, only one of the linkers is visible. I’m hoping you might be able to help me figure out what I’m doing wrong. Schrodenger support provided a recommendation. Part of it is to rename the protein chain to something else (e.g., chain F) so that it wouldn't interfere with chain A from the F-Actin chain. I’ve been unable to figure out how to change the name/ID of my chains. I have tried changing to “3 Button Viewing”, selecting “Chains”, clicking on the chain of interest, clicking on the selection “A” action button and selecting “rename selection”, as well as using the "set_name" command, but neither are working. Can anyone help me figure out what I’m doing wrong? Thanks so much! _______________________________________________ PyMOL-users mailing list Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=M7j0UHmKHyk5FNFceHpffMHdL3ng5zL6zrFUhJsbtHE&s=bELmqUjTG90kQgk8kBN8XAx-khyr8eDRjBdAfb4GoAs&e= Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=M7j0UHmKHyk5FNFceHpffMHdL3ng5zL6zrFUhJsbtHE&s=mh8suCHWbCtKsxU6HD2xWPPjtWMFzfLkFmQoahAqkrc&e= _______________________________________________ PyMOL-users mailing list Archives: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mail-2Darchive.com_pymol-2Dusers-40lists.sourceforge.net&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=J3kxkoyQ22CsHFbJcbFrSLohew1yxUPoqMUzfIEHcJU&s=AXD2c5dsooFjTkuWaXWQU3f1GXhdK7TncjbHewRu4XU&e= Unsubscribe: https://urldefense.proofpoint.com/v2/url?u=https-3A__sourceforge.net_projects_pymol_lists_pymol-2Dusers_unsubscribe&d=DwIGaQ&c=VjzId-SM5S6aVB_cCGQ0d3uo9UfKByQ3sI6Audoy6dY&r=k0gMbcsdOcdbPUNV5tW66KQSZfXL0ewVDPVBp7tqbks&m=J3kxkoyQ22CsHFbJcbFrSLohew1yxUPoqMUzfIEHcJU&s=rA1ZM4GK908qnxuClbB5y_2aKAA7EWem8fJrrDi1MD4&e= _______________________________________________ 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
