Re: [COOT] PDB parsing in coot 0.8.1 versus prior versions

[Jose Artur Brito]

Dear All, I was experiencing the same problem when reading pdb files with duplicate numbers so I tried this fix that Paul suggested. However, when I had that code line to the .coot file, here's what comes up: Loading ~/.coot...(set-find-hydrogen-torsion 1) Backtrace: In /home/jbrito/.coot:   29: 0* (allow-duplicate-sequence-numbers) /home/jbrito/.coot:29:1: In _expression_ (allow-duplicate-sequence-numbers): /home/jbrito/.coot:29:1: Unbound variable: allow-duplicate-sequence-numbers Gtk-Message: Failed to load module "canberra-gtk-module" Gtk-Message: Failed to load module "canberra-gtk-module" Gtk-Message: Failed to load module "overlay-scrollbar" Gtk-Message: Failed to load module "unity-gtk-module" Gtk-Message: Failed to load module "canberra-gtk-module" I am running Coot 0.8.1 (Turtle Bay), under Ubuntu 14.04 LTS. Any ideas what might be the issue here? Cheers, Jose On 03/27/2015 07:13 PM, Paul Emsley wrote: On 25/03/15 22:27, nih\mayerm wrote: Deal Paul. Recently I had an unusual case of dual occupancy of a ligand binding site by two different ligands. I refined this by giving same resids to the two ligands (here C1 in coordinates below), refining their occupancy (in Phenix) - worked very well. Older versions of COOT opened this PBD file just fine. Now, when I open in coot 0.8.1 I get the following error, and file cannot be opened. ERROR 42 READ: Duplicate sequence number and insertion code.           LINE #12921       HETATM 8309  N  BGLY C   1       9.972  61.351  43.716  0.24  9.17           N I realize my solution to the dual occupancy issue is a bit of a cludge (of which I was quite proud!) but I'm now forced to use an older version of coot when working with these files. Is the change a feature or a bug? It was a feature that stopped a bug (crash in a ccp4 library IIRC) in certain atom selections on chains that include duplicate sequence numbers. It seems that such files happen more often the I had realised and have since made it a user-setable option: Add this to your ~/.coot file (allow-duplicate-sequence-numbers) It's in the current 0.8.2-pre and and will be in 0.8.2 and later releases.  It's dangerous though. Paul. -- ************************************************ * José Artur Brito, PhD * * * * Post-Doctoral Fellow * * Membrane Protein Crystallography Lab * * Instituto de Tecnologia Química e Biológica * * Oeiras - Portugal * * * * Tel.: +351.21.446.97.61 * * Fax: +351.21.443.36.44 * * * * E-mail: jbr...@itqb.unl.pt * * URL: http://mx.itqb.unl.pt * ************************************************