Hi, I wanted to get some experience with a large model so I am exploring 4YBB.
Problem 1 If I select "Fetch PDB using Accession Code..." in the file menu and ask for 4YBB the download fails with PDB Accession Code: 4YBB BL WARNING:: Retrieve of url http://www.ebi.ac.uk/pdbe-srv/view/files/4ybb.ent failed handle_read_draw_molecule_with_recentre ("coot-download/4YBB.pdb.ent", 1) WARNING:: Error reading coot-download/4YBB.pdb.ent Clearly Coot is trying to download the old PDB format and not the new mmCIF. Problem 2 I downloaded 4ybb.cif from the RCSB site and loaded it into Coot via the "Open Coordinates..." option of the File menu. This loaded the model into the window and I can do all the mouse stuff I expect. I want to go to a specific location, however, so I opened the "Go To Atom..." dialog. If I select the QA chain in the chain box, there is no arrow to open the residue list. This seems to be the case for many RNA chains, although some like AA and AB do work. Protein chains seem to work fine. Even if I enter the chain, residue number, and atom name in the individual boxes the terminal window says that the atom cannot be found. WARNING:: atom with name "MG" alt-loc "", res-no: 3147, ins-code "", chain: "IN" not found in molecule 0 I have tried version 0.8.9.2 of either Coot on a CentOS 7 system or winCoot on a Windows 8.1 system. This model is a little large to just click around and hope to stumble upon the place I want to look at. Thanks for your help Dale Tronrud ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=COOT&A=1
