[Molvis-list] no chain designation

[timothy driscoll]

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
>
>OR
>
>you could try selecting by atom numbers instead of by residue numbers:
>
>  select atomno >= 1 & atomno < 999 # or whatever your atom numbers are
>


hi,

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.  :-(


regards,

tim
-- 
Timothy Driscoll
molvisions - see, grasp, learn.
<http://www.molvisions.com/>
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