On 05/03/2020 21:56, Dale Tronrud wrote:
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.
Thank you for the reminder. I will put it on the top of the list.
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
Sigh... I find parsing of the atom_site block so confusing. In this case, the atom_site.label_asym_id is not
the same as atom_site.auth_asym_id. IIRC, Coot and Coot users should be working with auth_asym_id symbols.
Having said that, the G chain is "empty" (from the Coot point of view) too - so something is going wrong.
I will look at this soon, but I fear that the problem lies in the bowels of
mmdb.
Paul.
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