[Molvis-list] no chain designation

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Tue Nov 16 12:10:23 EST 2004

On Tue, 16 Nov 2004, timothy driscoll wrote:

>On 2004-11-15 (16:44) Miguel wrote:
>>Rebecca wrote:
>>> I've got a molecule that has a propeptide but there are no chain
>>> designations in the file to distinguish this part of the molecule
>>> from the rest. So, when selecting a region (I'm trying to select
>>> only the first 62 amino acids that consistitute the propiece) PE
>>> selects the first 62 and also the next 62 (because the residue
>>> numbering system begins again from '1' at the '63rd' amino acid).
>>> Any ideas on how to get around this when no chain designations are
>>> provided?
>>I don't know what a propeptide is but ...
>>you could try:
>>  select amino & 1-62
>>you could try selecting by atom numbers instead of by residue numbers:
>>  select atomno >= 1 & atomno < 999 # or whatever your atom numbers are
>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).
>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.  but
>unfortunately, we could not even select these residues using 1P, 2P,
>etc., nor using resno=1P, etc.  :-(

I guess this is a PDB which breaks the PDB format definition? (using
'alternate location' indicator when an explicit chain id would be
better... or perhaps not?).

Would anyone consider setting up a PDBug site - i.e. a Bugzilla (or
similar) bug tracking system for PDB files which need attention in various

This would be a great 'check first' resource to help with this kind of


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