[phenixbb] constrain insertion codes to unit occupancy?

Georg Mlynek georg.mlynek at univie.ac.at
Sat Oct 15 15:39:35 PDT 2016

Dear Henry, you can find the answer here


example 5. Unfortunately 1EJG does not open in coot, because of a 
coordinate read error

ERROR 42 READ: Duplicate sequence number and insertion code.
          LINE #875
      ATOM    414  CA BSER A  22       6.034  13.399  -2.687  0.21 1.55

However pymol works.

The example is crambin

Here is pasted and changed a bit one sentence from the newsletter:

If residuenumber and chain ids are identical,while altloc are different, 
as well as residue names are allowed to be different.

So you have to remove

27 AChar iCode Code for insertion of residues.

this should work

ATOM   6500  CA ACYS B 101

ATOM   6490  CA BXXX B 101

Phenix will handle this then automatically.

Best regards, Georg.

On 10/15/2016 11:15 PM, van den Bedem, Henry wrote:
> Hi:
> I’m refining a site where there’s two compounds, each at partial 
> occupancy. I modeled that using alt codes and insertion codes 
> combined, like this
> ATOM   6500 CA ACYS B 101B
> ATOM   6490 CA BXXX B 101A
> How can I constrain the occupancies so that they sum to unity? I tried 
> several option, but the distinct insertions seem to refine 
> independently. Sorry if a similar question has been posted before, but 
> I could not find a solution searching phenixbb.
> Thanks!
> Henry
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