[Molvis-list] no chain designation

Miguel miguel at jmol.org
Tue Nov 16 12:59:00 EST 2004

Tim wrote:
> answered this offlist.  turns out the easiest way was by atomno range.
> a propeptide is a part of the protein that is cleaved during
> post-translational modification to give the active form of the enzyme
> (where it might be problematic to have the enzyme active before it is in
> the proper cellular location).

OK, thanks.

> the residue numbers for this propeptide (file 3PBH) are 1P-62P; the rest
> of the protein starts at residue 1.  note that the propiece residue
> numbers include the 'P'; this is not a chain designation.

These are insertion codes.

> but
> unfortunately, we could not even select these residues using 1P, 2P,

RasMol/Chime will interpret these as a chain identifier of 'P'

> etc., nor using resno=1P, etc.  :-(

RasMol/Chime does not handle them.

For those who may be wanting to work with this kind of thing in Jmol ...

Jmol handles insertion codes using a ^ caret syntax. The caret is required
to avoid ambiguity with a chain designation. So, in this case the syntax
to select the propeptide would be

  select 1^P-62^P

And saying

  select 62

Would select only residue 62, not residue 62^P


More information about the Molvis-list mailing list