[log in to unmask]" type="cite"> 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:

[log in to unmask]" type="cite">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.