Hi Marco, "Superpose" in *Coot* will also take any associated ligands along during the superposition. You can do this under "Calculate-> SSM Superpose". Be sure to check "move copy of moving structure". The one that moves will show as "copy of xxx", with xxx being the name of the one that was moved.
Then, after superposition, you can then change the chain of the extra protein (i.e., the one that has the DNA you want to put in your structure) to an unused chain ID and make sure your ligand also is assigned to an unused chain ID (Edit-> Change Chain IDs). Merge the two separate structures (Edit->Merge molecules). Finally, either in a text editor or even Pymol, remove the extraneous protein and save the new file. Best, Nick Clark On Tue, Feb 27, 2024 at 7:55 PM Marco Bravo <mbrav...@ucr.edu> wrote: > Hello all, > Does anyone know how to save a superimposed pymol or chimerax session as a > PDB file in correct format so that I can used it for ccp4 refmac? I am > trying to superimpose a protein with DNA bound onto the same protein from a > different species without the DNA. I just want the DNA from the protein-DNA > complex to be superimposed onto the apo protein structure. I have done the > superimposition and got rid of the protein from the original protein-DNA > complex and now have the DNA with the apo protein structure. When I try to > use this new PDB filer for refmac or even MR I get this error. Refmac: > Input coordinate file is not complete. Does anyone know how to properly do > this ? > > Thank you > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C2dbf6d888d0240f47ba508dc37f7e3d7%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638446785077487683%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=mZDceTaAWZwIFN3Kn2FsOEaweOkV8LPuCzM530v45ao%3D&reserved=0 > > This message was issued to members of > https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C2dbf6d888d0240f47ba508dc37f7e3d7%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638446785077487683%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=K1iVSXEgkOZp7evKeCDa7Ot%2BHISx8DaVa%2BYlRTLrx2w%3D&reserved=0, > a mailing list hosted by > https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C2dbf6d888d0240f47ba508dc37f7e3d7%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638446785077487683%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=UqDHxhOSIbmdNod%2BMugWF4nSyZyIt1kUhxPFwflboEs%3D&reserved=0, > terms & conditions are available at > https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F&data=05%7C02%7Cndclark2%40g-mail.buffalo.edu%7C2dbf6d888d0240f47ba508dc37f7e3d7%7C96464a8af8ed40b199e25f6b50a20250%7C0%7C0%7C638446785077487683%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=HSyOA2RStVQMsJKqQykBp9tekK8qs29a8QZwc7SUzPc%3D&reserved=0 > -- Nicholas D. Clark (He/Him) PhD Candidate Malkowski Lab University at Buffalo Department of Structural Biology Jacob's School of Medicine & Biomedical Sciences 955 Main Street, RM 5130 Buffalo, NY 14203 Cell: 716-830-1908 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
